Internet Anonymity: Pew: Privacy.Importance regression:: Anonymity2
bdanalytics
Date: (Fri) Jun 12, 2015
Introduction:
Data: Source: Training: https://courses.edx.org/asset-v1:MITx+15.071x_2a+2T2015+type@asset+block/AnonymityPoll.csv
New:
Time period:
Synopsis:
Based on analysis utilizing <> techniques,
[](.png)
Potential next steps include:
- Organization:
- Categorize by chunk
- Priority criteria:
- Ease of change
- Impacts report
- Cleans innards
- Bug report
- all chunks:
- at chunk-end rm(!glb_)
- manage.missing.data chunk:
- cleaner way to manage re-splitting of training vs. new entity
- extract.features chunk:
- Add n-grams for glb_txt_vars
- “RTextTools”, “tau”, “RWeka”, and “textcat” packages
- Convert user-specified mutate code to config specs
- Add n-grams for glb_txt_vars
- fit.models chunk:
- Prediction accuracy scatter graph:
- Add tiles (raw vs. PCA)
- Use shiny for drop-down of “important” features
Use plot.ly for interactive plots ?
- Change .fit suffix of model metrics to .mdl if it’s data independent (e.g. AIC, Adj.R.Squared - is it truly data independent ?, etc.)
- move model_type parameter to myfit_mdl before indep_vars_vctr (keep all model_* together)
- create a custom model for rpart that has minbucket as a tuning parameter
varImp for randomForest crashes in caret version:6.0.41 -> submit bug report
- Probability handling for multinomials vs. desired binomial outcome
- ROCR currently supports only evaluation of binary classification tasks (version 1.0.7)
extensions toward multiclass classification are scheduled for the next release
- Skip trControl.method=“cv” for dummy classifier ?
- Add custom model to caret for a dummy (baseline) classifier (binomial & multinomial) that generates proba/outcomes which mimics the freq distribution of glb_rsp_var values; Right now glb_dmy_glm_mdl always generates most frequent outcome in training data
glm_dmy_mdl should use the same method as glm_sel_mdl until custom dummy classifer is implemented
- fit.all.training chunk:
- myplot_prediction_classification: displays ‘x’ instead of ‘+’ when there are no prediction errors
- Compare glb_sel_mdl vs. glb_fin_mdl:
- varImp
- Prediction differences (shd be minimal ?)
- Move glb_analytics_diag_plots to mydsutils.R: (+) Easier to debug (-) Too many glb vars used
- Add print(ggplot.petrinet(glb_analytics_pn) + coord_flip()) at the end of every major chunk
- Parameterize glb_analytics_pn
- Move glb_impute_missing_data to mydsutils.R: (-) Too many glb vars used; glb_<>_df reassigned
- Replicate myfit_mdl_classification features in myfit_mdl_regression
- Do non-glm methods handle interaction terms ?
- f-score computation for classifiers should be summation across outcomes (not just the desired one ?)
- Add accuracy computation to glb_dmy_mdl in predict.data.new chunk
- Why does splitting fit.data.training.all chunk into separate chunks add an overhead of ~30 secs ? It’s not rbind b/c other chunks have lower elapsed time. Is it the number of plots ?
- Incorporate code chunks in print_sessionInfo
- Test against
- projects in github.com/bdanalytics
- lectures in jhu-datascience track
Analysis:
rm(list=ls())
set.seed(12345)
options(stringsAsFactors=FALSE)
source("~/Dropbox/datascience/R/myscript.R")
source("~/Dropbox/datascience/R/mydsutils.R")## Loading required package: caret
## Loading required package: lattice
## Loading required package: ggplot2source("~/Dropbox/datascience/R/myplot.R")
source("~/Dropbox/datascience/R/mypetrinet.R")
source("~/Dropbox/datascience/R/myplclust.R")
# Gather all package requirements here
suppressPackageStartupMessages(require(doMC))
registerDoMC(4) # max(length(glb_txt_vars), glb_n_cv_folds) + 1
#packageVersion("snow")
#require(sos); findFn("cosine", maxPages=2, sortby="MaxScore")
# Analysis control global variables
glb_trnng_url <- "https://courses.edx.org/asset-v1:MITx+15.071x_2a+2T2015+type@asset+block/AnonymityPoll.csv"
glb_newdt_url <- "<newdt_url>"
glb_out_pfx <- "Anonymity2_"
glb_save_envir <- FALSE # or TRUE
glb_is_separate_newent_dataset <- FALSE # or TRUE
glb_split_entity_newent_datasets <- TRUE # or FALSE
glb_split_newdata_method <- "sample" # "condition" or "sample" or "copy"
glb_split_newdata_condition <- NULL # or "is.na(<var>)"; "<var> <condition_operator> <value>"
glb_split_newdata_size_ratio <- 0.3 # > 0 & < 1
glb_split_sample.seed <- 123 # or any integer
glb_drop_vars <- c(NULL) # or c("<col_name>")
glb_max_fitent_obs <- NULL # or any integer
glb_is_regression <- TRUE; glb_is_classification <- FALSE; glb_is_binomial <- TRUE
glb_rsp_var_raw <- "Privacy.Importance"
# for classification, the response variable has to be a factor
glb_rsp_var <- glb_rsp_var_raw # or "Privacy.Importance.fctr"
# if the response factor is based on numbers/logicals e.g (0/1 OR TRUE/FALSE vs. "A"/"B"),
# or contains spaces (e.g. "Not in Labor Force")
# caret predict(..., type="prob") crashes
glb_map_rsp_raw_to_var <- NULL # or function(raw) {
#relevel(factor(ifelse(raw == 1, "Y", "N")), as.factor(c("Y", "N")), ref="N")
#as.factor(paste0("B", raw))
#as.factor(gsub(" ", "\\.", raw))
#}
#glb_map_rsp_raw_to_var(c(1, 1, 0, 0, 0))
glb_map_rsp_var_to_raw <- NULL # or function(var) {
#as.numeric(var) - 1
#as.numeric(var)
#gsub("\\.", " ", levels(var)[as.numeric(var)])
#c(" <=50K", " >50K")[as.numeric(var)]
#c(FALSE, TRUE)[as.numeric(var)]
#}
#glb_map_rsp_var_to_raw(glb_map_rsp_raw_to_var(c(1, 1, 0, 0, 0)))
if ((glb_rsp_var != glb_rsp_var_raw) & is.null(glb_map_rsp_raw_to_var))
stop("glb_map_rsp_raw_to_var function expected")
glb_rsp_var_out <- paste0(glb_rsp_var, ".predict.") # model_id is appended later
# List info gathered for various columns
# <col_name>: <description>; <notes>
# Internet.Use: A binary variable indicating if the interviewee uses the Internet, at least occasionally (equals 1 if the interviewee uses the Internet, and equals 0 if the interviewee does not use the Internet).
# Smartphone: A binary variable indicating if the interviewee has a smartphone (equals 1 if they do have a smartphone, and equals 0 if they don't have a smartphone).
# Sex: Male or Female.
# Age: Age in years.
# State: State of residence of the interviewee.
# Region: Census region of the interviewee (Midwest, Northeast, South, or West).
# Conservativeness: Self-described level of conservativeness of interviewee, from 1 (very liberal) to 5 (very conservative).
# Info.On.Internet: Number of the following items this interviewee believes to be available on the Internet for others to see: (1) Their email address; (2) Their home address; (3) Their home phone number; (4) Their cell phone number; (5) The employer/company they work for; (6) Their political party or political affiliation; (7) Things they've written that have their name on it; (8) A photo of them; (9) A video of them; (10) Which groups or organizations they belong to; and (11) Their birth date.
# Worry.About.Info: A binary variable indicating if the interviewee worries about how much information is available about them on the Internet (equals 1 if they worry, and equals 0 if they don't worry).
# Privacy.Importance: A score from 0 (privacy is not too important) to 100 (privacy is very important), which combines the degree to which they find privacy important in the following: (1) The websites they browse; (2) Knowledge of the place they are located when they use the Internet; (3) The content and files they download; (4) The times of day they are online; (5) The applications or programs they use; (6) The searches they perform; (7) The content of their email; (8) The people they exchange email with; and (9) The content of their online chats or hangouts with others.
# Anonymity.Possible: A binary variable indicating if the interviewee thinks it's possible to use the Internet anonymously, meaning in such a way that online activities can't be traced back to them (equals 1 if he/she believes you can, and equals 0 if he/she believes you can't).
# Tried.Masking.Identity: A binary variable indicating if the interviewee has ever tried to mask his/her identity when using the Internet (equals 1 if he/she has tried to mask his/her identity, and equals 0 if he/she has not tried to mask his/her identity).
# Privacy.Laws.Effective: A binary variable indicating if the interviewee believes United States law provides reasonable privacy protection for Internet users (equals 1 if he/she believes it does, and equals 0 if he/she believes it doesn't).
# If multiple vars are parts of id, consider concatenating them to create one id var
# If glb_id_var == NULL, ".rownames <- row.names()" is the default
glb_id_var <- NULL # or c("<var1>")
glb_category_vars <- NULL # or c("<var1>", "<var2>")
glb_map_vars <- NULL # or c("<var1>", "<var2>")
glb_map_urls <- list();
# glb_map_urls[["<var1>"]] <- "<var1.url>"
glb_assign_pairs_lst <- NULL;
glb_assign_pairs_lst[["Internet.Use"]] <- list(from=c(NA),
to=c(0))
glb_assign_vars <- names(glb_assign_pairs_lst)
glb_transform_lst <- NULL;
glb_transform_lst[["Age"]] <- list(
mapfn=function(raw) { tfr_raw <- as.character(cut(raw, 5));
tfr_raw[is.na(tfr_raw)] <- "NA.my";
return(as.factor(tfr_raw)) }
, sfx=".my.fctr")
# mapfn(glb_allobs_df$Age)
glb_transform_lst[["Anonymity.Possible"]] <- list(
mapfn=function(raw) { tfr_raw <- as.character(raw); tfr_raw[is.na(tfr_raw)] <- "NA.my";
return(as.factor(tfr_raw)) }
, sfx=".my.fctr")
# mapfn(glb_allobs_df$Anonymity.Possible)
glb_transform_lst[["Conservativeness"]] <- list(
mapfn=function(raw) { tfr_raw <- as.character(raw); tfr_raw[is.na(tfr_raw)] <- "NA.my";
return(as.factor(tfr_raw)) }
, sfx=".my.fctr")
# mapfn(glb_allobs_df$Conservativeness)
glb_transform_lst[["Info.On.Internet"]] <- list(
mapfn=function(raw) { tfr_raw <- as.character(raw); tfr_raw[is.na(tfr_raw)] <- "NA.my";
return(as.factor(tfr_raw)) }
, sfx=".my.fctr")
# mapfn(glb_allobs_df$Info.On.Internet)
glb_transform_lst[["Privacy.Laws.Effective"]] <- list(
mapfn=function(raw) { tfr_raw <- as.character(raw); tfr_raw[is.na(tfr_raw)] <- "NA.my";
return(as.factor(tfr_raw)) }
, sfx=".my.fctr")
# mapfn(glb_allobs_df$Privacy.Laws.Effective)
glb_transform_lst[["Smartphone"]] <- list(
mapfn=function(raw) { tfr_raw <- as.character(raw); tfr_raw[is.na(tfr_raw)] <- "NA.my";
return(as.factor(tfr_raw)) }
, sfx=".my.fctr")
# mapfn(glb_allobs_df$Smartphone)
glb_transform_lst[["Tried.Masking.Identity"]] <- list(
mapfn=function(raw) { tfr_raw <- as.character(raw); tfr_raw[is.na(tfr_raw)] <- "NA.my";
return(as.factor(tfr_raw)) }
, sfx=".my.fctr")
# mapfn(glb_allobs_df$Tried.Masking.Identity)
glb_transform_lst[["Worry.About.Info"]] <- list(
mapfn=function(raw) { tfr_raw <- as.character(raw); tfr_raw[is.na(tfr_raw)] <- "NA.my";
return(as.factor(tfr_raw)) }
, sfx=".my.fctr")
# mapfn(glb_allobs_df$Worry.About.Info)
# Add logs of numerics that are not distributed normally -> do automatically ???
glb_transform_vars <- names(glb_transform_lst)
glb_date_vars <- NULL # or c("<date_var>")
glb_date_fmts <- list(); #glb_date_fmts[["<date_var>"]] <- "%m/%e/%y"
glb_date_tzs <- list(); #glb_date_tzs[["<date_var>"]] <- "America/New_York"
#grep("America/New", OlsonNames(), value=TRUE)
glb_txt_vars <- NULL # or c("<txt_var1>", "<txt_var2>")
#Sys.setlocale("LC_ALL", "C") # For english
glb_append_stop_words <- list()
# Remember to use unstemmed words
#orderBy(~ -cor.y.abs, subset(glb_feats_df, grepl("[HSA]\\.T\\.", id) & !is.na(cor.high.X)))
#dsp_obs(Headline.contains="polit")
#subset(glb_allobs_df, H.T.compani > 0)[, c("UniqueID", "Headline", "H.T.compani")]
# glb_append_stop_words[["<txt_var1>"]] <- c(NULL
# # ,"<word1>" # <reason1>
# )
#subset(glb_allobs_df, S.T.newyorktim > 0)[, c("UniqueID", "Snippet", "S.T.newyorktim")]
#glb_txt_lst[["Snippet"]][which(glb_allobs_df$UniqueID %in% c(8394, 8317, 8339, 8350, 8307))]
glb_important_terms <- list()
# Remember to use stemmed terms
glb_sprs_thresholds <- NULL # or c(0.988, 0.970, 0.970) # Generates 29, 22, 22 terms
# Properties:
# numrows(glb_feats_df) << numrows(glb_fitobs_df)
# Select terms that appear in at least 0.2 * O(FP/FN(glb_OOBobs_df))
# numrows(glb_OOBobs_df) = 1.1 * numrows(glb_newobs_df)
names(glb_sprs_thresholds) <- glb_txt_vars
# User-specified exclusions
glb_exclude_vars_as_features <- c("State.fctr") # or c("<var_name>")
if (glb_rsp_var_raw != glb_rsp_var)
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features,
glb_rsp_var_raw)
# List feats that shd be excluded due to known causation by prediction variable
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features,
c(NULL)) # or c("<col_name>")
glb_impute_na_data <- FALSE # or TRUE
glb_mice_complete.seed <- 144 # or any integer
glb_cluster <- FALSE # or TRUE
glb_interaction_only_features <- NULL # or ???
glb_models_lst <- list(); glb_models_df <- data.frame()
# Regression
if (glb_is_regression)
glb_models_method_vctr <- c("lm", "glm", "bayesglm", "rpart", "rf") else
# Classification
if (glb_is_binomial)
glb_models_method_vctr <- c("glm", "bayesglm", "rpart", "rf") else
glb_models_method_vctr <- c("rpart", "rf")
# Baseline prediction model feature(s)
glb_Baseline_mdl_var <- NULL # or c("<col_name>")
glb_model_metric_terms <- NULL # or matrix(c(
# 0,1,2,3,4,
# 2,0,1,2,3,
# 4,2,0,1,2,
# 6,4,2,0,1,
# 8,6,4,2,0
# ), byrow=TRUE, nrow=5)
glb_model_metric <- NULL # or "<metric_name>"
glb_model_metric_maximize <- NULL # or FALSE (TRUE is not the default for both classification & regression)
glb_model_metric_smmry <- NULL # or function(data, lev=NULL, model=NULL) {
# confusion_mtrx <- t(as.matrix(confusionMatrix(data$pred, data$obs)))
# #print(confusion_mtrx)
# #print(confusion_mtrx * glb_model_metric_terms)
# metric <- sum(confusion_mtrx * glb_model_metric_terms) / nrow(data)
# names(metric) <- glb_model_metric
# return(metric)
# }
glb_tune_models_df <-
rbind(
#data.frame(parameter="cp", min=0.00005, max=0.00005, by=0.000005),
#seq(from=0.01, to=0.01, by=0.01)
#data.frame(parameter="mtry", min=080, max=100, by=10),
#data.frame(parameter="mtry", min=08, max=10, by=1),
data.frame(parameter="dummy", min=2, max=4, by=1)
)
# or NULL
glb_n_cv_folds <- 3 # or NULL
glb_clf_proba_threshold <- NULL # 0.5
# Model selection criteria
if (glb_is_regression)
glb_model_evl_criteria <- c("min.RMSE.OOB", "max.R.sq.OOB", "max.Adj.R.sq.fit")
if (glb_is_classification) {
if (glb_is_binomial)
glb_model_evl_criteria <-
c("max.Accuracy.OOB", "max.auc.OOB", "max.Kappa.OOB", "min.aic.fit") else
glb_model_evl_criteria <- c("max.Accuracy.OOB", "max.Kappa.OOB")
}
glb_sel_mdl_id <- NULL # or "<model_id_prefix>.<model_method>"
glb_fin_mdl_id <- glb_sel_mdl_id # or "Final"
# Depict process
glb_analytics_pn <- petrinet(name="glb_analytics_pn",
trans_df=data.frame(id=1:6,
name=c("data.training.all","data.new",
"model.selected","model.final",
"data.training.all.prediction","data.new.prediction"),
x=c( -5,-5,-15,-25,-25,-35),
y=c( -5, 5, 0, 0, -5, 5)
),
places_df=data.frame(id=1:4,
name=c("bgn","fit.data.training.all","predict.data.new","end"),
x=c( -0, -20, -30, -40),
y=c( 0, 0, 0, 0),
M0=c( 3, 0, 0, 0)
),
arcs_df=data.frame(
begin=c("bgn","bgn","bgn",
"data.training.all","model.selected","fit.data.training.all",
"fit.data.training.all","model.final",
"data.new","predict.data.new",
"data.training.all.prediction","data.new.prediction"),
end =c("data.training.all","data.new","model.selected",
"fit.data.training.all","fit.data.training.all","model.final",
"data.training.all.prediction","predict.data.new",
"predict.data.new","data.new.prediction",
"end","end")
))
#print(ggplot.petrinet(glb_analytics_pn))
print(ggplot.petrinet(glb_analytics_pn) + coord_flip())## Loading required package: grid
glb_analytics_avl_objs <- NULL
glb_chunks_df <- myadd_chunk(NULL, "import.data")## label step_major step_minor bgn end elapsed
## 1 import.data 1 0 9.118 NA NAStep 1.0: import data
chunk option: eval=
glb_trnobs_df <- myimport_data(url=glb_trnng_url, comment="glb_trnobs_df",
force_header=TRUE)## [1] "Reading file ./data/AnonymityPoll.csv..."
## [1] "dimensions of data in ./data/AnonymityPoll.csv: 1,002 rows x 13 cols"
## Internet.Use Smartphone Sex Age State Region
## 1 1 0 Male 62 Massachusetts Northeast
## 2 1 0 Male 45 South Carolina South
## 3 0 1 Female 70 New Jersey Northeast
## 4 1 0 Male 70 Georgia South
## 5 0 NA Female 80 Georgia South
## 6 1 1 Male 49 Tennessee South
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 1 4 0 1 100.00000
## 2 1 1 0 0.00000
## 3 4 0 0 NA
## 4 4 3 1 88.88889
## 5 4 NA NA NA
## 6 4 6 0 88.88889
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 1 0 0 0
## 2 1 0 1
## 3 0 0 NA
## 4 1 0 0
## 5 NA NA NA
## 6 1 1 0
## Internet.Use Smartphone Sex Age State Region
## 35 1 0 Female 74 Florida South
## 153 0 0 Female 77 Oregon West
## 511 1 1 Male 19 Virginia South
## 729 0 1 Male 52 Connecticut Northeast
## 734 1 1 Male 26 Wisconsin Midwest
## 990 1 1 Female 36 Missouri Midwest
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 35 3 0 0 6.25
## 153 3 NA NA NA
## 511 3 7 0 100.00
## 729 2 1 0 50.00
## 734 5 2 0 100.00
## 990 3 6 0 100.00
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 35 0 0 0
## 153 NA NA NA
## 511 1 0 0
## 729 1 0 1
## 734 0 0 0
## 990 0 0 1
## Internet.Use Smartphone Sex Age State Region Conservativeness
## 997 1 1 Male 29 California West 3
## 998 1 1 Female 57 Utah West 4
## 999 0 NA Male 29 Colorado West 3
## 1000 1 1 Male 22 California West 4
## 1001 0 0 Female 63 California West 4
## 1002 1 1 Female 26 Texas South 3
## Info.On.Internet Worry.About.Info Privacy.Importance
## 997 7 1 77.77778
## 998 7 1 27.77778
## 999 NA NA NA
## 1000 6 0 11.11111
## 1001 NA NA NA
## 1002 3 1 55.55556
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 997 1 1 1
## 998 0 0 1
## 999 NA NA 0
## 1000 0 0 1
## 1001 NA NA 1
## 1002 0 0 0
## 'data.frame': 1002 obs. of 13 variables:
## $ Internet.Use : int 1 1 0 1 0 1 1 0 0 1 ...
## $ Smartphone : int 0 0 1 0 NA 1 0 0 NA 0 ...
## $ Sex : chr "Male" "Male" "Female" "Male" ...
## $ Age : int 62 45 70 70 80 49 52 76 75 76 ...
## $ State : chr "Massachusetts" "South Carolina" "New Jersey" "Georgia" ...
## $ Region : chr "Northeast" "South" "Northeast" "South" ...
## $ Conservativeness : int 4 1 4 4 4 4 3 3 4 4 ...
## $ Info.On.Internet : int 0 1 0 3 NA 6 3 NA NA 0 ...
## $ Worry.About.Info : int 1 0 0 1 NA 0 1 NA NA 0 ...
## $ Privacy.Importance : num 100 0 NA 88.9 NA ...
## $ Anonymity.Possible : int 0 1 0 1 NA 1 0 NA NA 1 ...
## $ Tried.Masking.Identity: int 0 0 0 0 NA 1 0 NA NA 0 ...
## $ Privacy.Laws.Effective: int 0 1 NA 0 NA 0 1 NA 0 1 ...
## - attr(*, "comment")= chr "glb_trnobs_df"
## NULL# glb_trnobs_df <- data.frame()
# for (symbol in c("Boeing", "CocaCola", "GE", "IBM", "ProcterGamble")) {
# sym_trnobs_df <-
# myimport_data(url=gsub("IBM", symbol, glb_trnng_url), comment="glb_trnobs_df",
# force_header=TRUE)
# sym_trnobs_df$Symbol <- symbol
# glb_trnobs_df <- myrbind_df(glb_trnobs_df, sym_trnobs_df)
# }
if (glb_is_separate_newent_dataset) {
glb_newobs_df <- myimport_data(url=glb_newdt_url, comment="glb_newobs_df",
force_header=TRUE)
# To make plots / stats / checks easier in chunk:inspectORexplore.data
glb_allobs_df <- myrbind_df(glb_trnobs_df, glb_newobs_df);
comment(glb_allobs_df) <- "glb_allobs_df"
} else {
glb_allobs_df <- glb_trnobs_df; comment(glb_allobs_df) <- "glb_allobs_df"
if (!glb_split_entity_newent_datasets) {
stop("Not implemented yet")
glb_newobs_df <- glb_trnobs_df[sample(1:nrow(glb_trnobs_df),
max(2, nrow(glb_trnobs_df) / 1000)),]
} else if (glb_split_newdata_method == "condition") {
glb_newobs_df <- do.call("subset",
list(glb_trnobs_df, parse(text=glb_split_newdata_condition)))
glb_trnobs_df <- do.call("subset",
list(glb_trnobs_df, parse(text=paste0("!(",
glb_split_newdata_condition,
")"))))
} else if (glb_split_newdata_method == "sample") {
require(caTools)
set.seed(glb_split_sample.seed)
split <- sample.split(glb_trnobs_df[, glb_rsp_var_raw],
SplitRatio=(1-glb_split_newdata_size_ratio))
glb_newobs_df <- glb_trnobs_df[!split, ]
glb_trnobs_df <- glb_trnobs_df[split ,]
} else if (glb_split_newdata_method == "copy") {
glb_trnobs_df <- glb_allobs_df
comment(glb_trnobs_df) <- "glb_trnobs_df"
glb_newobs_df <- glb_allobs_df
comment(glb_newobs_df) <- "glb_newobs_df"
} else stop("glb_split_newdata_method should be %in% c('condition', 'sample', 'copy')")
comment(glb_newobs_df) <- "glb_newobs_df"
myprint_df(glb_newobs_df)
str(glb_newobs_df)
if (glb_split_entity_newent_datasets) {
myprint_df(glb_trnobs_df)
str(glb_trnobs_df)
}
} ## Loading required package: caTools## Internet.Use Smartphone Sex Age State Region
## 3 0 1 Female 70 New Jersey Northeast
## 4 1 0 Male 70 Georgia South
## 5 0 NA Female 80 Georgia South
## 7 1 0 Female 52 Michigan Midwest
## 8 0 0 Female 76 New York Northeast
## 9 0 NA Male 75 North Carolina South
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 3 4 0 0 NA
## 4 4 3 1 88.88889
## 5 4 NA NA NA
## 7 3 3 1 33.33333
## 8 3 NA NA NA
## 9 4 NA NA NA
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 3 0 0 NA
## 4 1 0 0
## 5 NA NA NA
## 7 0 0 1
## 8 NA NA NA
## 9 NA NA 0
## Internet.Use Smartphone Sex Age State Region
## 13 0 0 Male 72 New York Northeast
## 179 0 0 Female 90 Michigan Midwest
## 230 0 0 Female 80 Kentucky South
## 499 0 0 Female 72 Kentucky South
## 905 1 1 Female 61 Massachusetts Northeast
## 923 1 0 Male 55 California West
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 13 5 NA NA NA
## 179 4 NA NA NA
## 230 NA NA NA NA
## 499 3 NA NA NA
## 905 3 6 1 61.11111
## 923 4 6 0 33.33333
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 13 NA NA 1
## 179 NA NA NA
## 230 NA NA NA
## 499 NA NA 0
## 905 0 0 1
## 923 1 0 0
## Internet.Use Smartphone Sex Age State Region Conservativeness
## 988 1 1 Male 45 Louisiana South 3
## 994 1 1 Male 18 Oklahoma South 3
## 996 1 1 Female 30 Arizona West 2
## 997 1 1 Male 29 California West 3
## 999 0 NA Male 29 Colorado West 3
## 1001 0 0 Female 63 California West 4
## Info.On.Internet Worry.About.Info Privacy.Importance
## 988 2 1 100.00000
## 994 7 0 44.44444
## 996 5 0 94.44444
## 997 7 1 77.77778
## 999 NA NA NA
## 1001 NA NA NA
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 988 0 0 0
## 994 0 0 0
## 996 1 0 0
## 997 1 1 1
## 999 NA NA 0
## 1001 NA NA 1
## 'data.frame': 446 obs. of 13 variables:
## $ Internet.Use : int 0 1 0 1 0 0 1 0 0 0 ...
## $ Smartphone : int 1 0 NA 0 0 NA 0 0 0 0 ...
## $ Sex : chr "Female" "Male" "Female" "Female" ...
## $ Age : int 70 70 80 52 76 75 76 69 72 63 ...
## $ State : chr "New Jersey" "Georgia" "Georgia" "Michigan" ...
## $ Region : chr "Northeast" "South" "South" "Midwest" ...
## $ Conservativeness : int 4 4 4 3 3 4 4 4 5 3 ...
## $ Info.On.Internet : int 0 3 NA 3 NA NA 0 NA NA NA ...
## $ Worry.About.Info : int 0 1 NA 1 NA NA 0 NA NA NA ...
## $ Privacy.Importance : num NA 88.9 NA 33.3 NA ...
## $ Anonymity.Possible : int 0 1 NA 0 NA NA 1 NA NA NA ...
## $ Tried.Masking.Identity: int 0 0 NA 0 NA NA 0 NA NA NA ...
## $ Privacy.Laws.Effective: int NA 0 NA 1 NA 0 1 0 1 0 ...
## - attr(*, "comment")= chr "glb_newobs_df"
## Internet.Use Smartphone Sex Age State Region
## 1 1 0 Male 62 Massachusetts Northeast
## 2 1 0 Male 45 South Carolina South
## 6 1 1 Male 49 Tennessee South
## 12 1 1 Female 50 Virginia South
## 14 1 1 Female 47 North Carolina South
## 15 1 0 Male 69 New York Northeast
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 1 4 0 1 100.00000
## 2 1 1 0 0.00000
## 6 4 6 0 88.88889
## 12 3 1 0 27.77778
## 14 3 0 0 0.00000
## 15 3 9 0 77.77778
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 1 0 0 0
## 2 1 0 1
## 6 1 1 0
## 12 0 0 0
## 14 1 0 0
## 15 0 0 0
## Internet.Use Smartphone Sex Age State Region Conservativeness
## 121 1 1 Female 55 California West 3
## 322 1 1 Female 43 Michigan Midwest 3
## 393 0 1 Male 72 Washington West 3
## 439 1 NA Female 67 Kansas Midwest 4
## 521 1 1 Male 34 Minnesota Midwest 4
## 815 1 1 Male 46 California West NA
## Info.On.Internet Worry.About.Info Privacy.Importance
## 121 6 1 61.11111
## 322 8 1 100.00000
## 393 2 1 100.00000
## 439 2 0 43.75000
## 521 6 0 0.00000
## 815 7 1 100.00000
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 121 0 0 1
## 322 0 0 1
## 393 0 0 0
## 439 0 0 NA
## 521 1 0 1
## 815 0 1 NA
## Internet.Use Smartphone Sex Age State Region
## 992 1 1 Male 37 Texas South
## 993 1 1 Female 63 Wisconsin Midwest
## 995 1 1 Female 55 Colorado West
## 998 1 1 Female 57 Utah West
## 1000 1 1 Male 22 California West
## 1002 1 1 Female 26 Texas South
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 992 1 2 0 50.00000
## 993 2 0 0 83.33333
## 995 3 3 1 88.88889
## 998 4 7 1 27.77778
## 1000 4 6 0 11.11111
## 1002 3 3 1 55.55556
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 992 1 0 0
## 993 0 0 1
## 995 0 0 0
## 998 0 0 1
## 1000 0 0 1
## 1002 0 0 0
## 'data.frame': 556 obs. of 13 variables:
## $ Internet.Use : int 1 1 1 1 1 1 1 1 1 1 ...
## $ Smartphone : int 0 0 1 1 1 0 0 0 0 0 ...
## $ Sex : chr "Male" "Male" "Male" "Female" ...
## $ Age : int 62 45 49 50 47 69 91 66 61 58 ...
## $ State : chr "Massachusetts" "South Carolina" "Tennessee" "Virginia" ...
## $ Region : chr "Northeast" "South" "South" "South" ...
## $ Conservativeness : int 4 1 4 3 3 3 5 5 3 5 ...
## $ Info.On.Internet : int 0 1 6 1 0 9 5 2 1 1 ...
## $ Worry.About.Info : int 1 0 0 0 0 0 1 0 0 0 ...
## $ Privacy.Importance : num 100 0 88.9 27.8 0 ...
## $ Anonymity.Possible : int 0 1 1 0 1 0 NA 1 0 0 ...
## $ Tried.Masking.Identity: int 0 0 1 0 0 0 0 0 0 0 ...
## $ Privacy.Laws.Effective: int 0 1 0 0 0 0 0 0 0 0 ...
## - attr(*, "comment")= chr "glb_trnobs_df"if ((num_nas <- sum(is.na(glb_trnobs_df[, glb_rsp_var_raw]))) > 0)
stop("glb_trnobs_df$", glb_rsp_var_raw, " contains NAs for ", num_nas, " obs")
if (nrow(glb_trnobs_df) == nrow(glb_allobs_df))
warning("glb_trnobs_df same as glb_allobs_df")
if (nrow(glb_newobs_df) == nrow(glb_allobs_df))
warning("glb_newobs_df same as glb_allobs_df")
if (length(glb_drop_vars) > 0) {
warning("dropping vars: ", paste0(glb_drop_vars, collapse=", "))
glb_allobs_df <- glb_allobs_df[, setdiff(names(glb_allobs_df), glb_drop_vars)]
glb_trnobs_df <- glb_trnobs_df[, setdiff(names(glb_trnobs_df), glb_drop_vars)]
glb_newobs_df <- glb_newobs_df[, setdiff(names(glb_newobs_df), glb_drop_vars)]
}
#stop(here"); sav_allobs_df <- glb_allobs_df # glb_allobs_df <- sav_allobs_df
# Check for duplicates in glb_id_var
if (length(glb_id_var) == 0) {
warning("using .rownames as identifiers for observations")
glb_allobs_df$.rownames <- rownames(glb_allobs_df)
glb_trnobs_df$.rownames <- rownames(glb_trnobs_df)
glb_newobs_df$.rownames <- rownames(glb_newobs_df)
glb_id_var <- ".rownames"
}## Warning: using .rownames as identifiers for observationsif (sum(duplicated(glb_allobs_df[, glb_id_var, FALSE])) > 0)
stop(glb_id_var, " duplicated in glb_allobs_df")
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, glb_id_var)
# Combine trnent & newent into glb_allobs_df for easier manipulation
glb_trnobs_df$.src <- "Train"; glb_newobs_df$.src <- "Test";
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, ".src")
glb_allobs_df <- myrbind_df(glb_trnobs_df, glb_newobs_df)
comment(glb_allobs_df) <- "glb_allobs_df"
glb_allobs_df <- orderBy(reformulate(glb_id_var), glb_allobs_df)
glb_trnobs_df <- glb_newobs_df <- NULL
glb_chunks_df <- myadd_chunk(glb_chunks_df, "inspect.data", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 1 import.data 1 0 9.118 9.966 0.848
## 2 inspect.data 2 0 9.966 NA NAStep 2.0: inspect data
#print(str(glb_allobs_df))
#View(glb_allobs_df)
dsp_class_dstrb <- function(var) {
xtab_df <- mycreate_xtab_df(glb_allobs_df, c(".src", var))
rownames(xtab_df) <- xtab_df$.src
xtab_df <- subset(xtab_df, select=-.src)
print(xtab_df)
print(xtab_df / rowSums(xtab_df, na.rm=TRUE))
}
# Performed repeatedly in other chunks
glb_chk_data <- function() {
# Histogram of predictor in glb_trnobs_df & glb_newobs_df
print(myplot_histogram(glb_allobs_df, glb_rsp_var_raw) + facet_wrap(~ .src))
if (glb_is_classification)
dsp_class_dstrb(var=ifelse(glb_rsp_var %in% names(glb_allobs_df),
glb_rsp_var, glb_rsp_var_raw))
mycheck_problem_data(glb_allobs_df)
}
glb_chk_data()
## [1] "numeric data missing in glb_allobs_df: "
## Internet.Use Smartphone Age
## 1 43 27
## Conservativeness Info.On.Internet Worry.About.Info
## 62 210 212
## Privacy.Importance Anonymity.Possible Tried.Masking.Identity
## 215 249 218
## Privacy.Laws.Effective
## 108
## [1] "numeric data w/ 0s in glb_allobs_df: "
## Internet.Use Smartphone Info.On.Internet
## 226 472 105
## Worry.About.Info Privacy.Importance Anonymity.Possible
## 404 43 475
## Tried.Masking.Identity Privacy.Laws.Effective
## 656 660
## [1] "numeric data w/ Infs in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ NaNs in glb_allobs_df: "
## named integer(0)
## [1] "string data missing in glb_allobs_df: "
## Sex State Region .rownames
## 0 0 0 0# Create new features that help diagnostics
if (!is.null(glb_map_rsp_raw_to_var)) {
glb_allobs_df[, glb_rsp_var] <-
glb_map_rsp_raw_to_var(glb_allobs_df[, glb_rsp_var_raw])
mycheck_map_results(mapd_df=glb_allobs_df,
from_col_name=glb_rsp_var_raw, to_col_name=glb_rsp_var)
if (glb_is_classification) dsp_class_dstrb(glb_rsp_var)
}
# Convert dates to numbers
# typically, dates come in as chars;
# so this must be done before converting chars to factors
myextract_dates_df <- function(df, vars, id_vars, rsp_var) {
keep_feats <- c(NULL)
for (var in vars) {
dates_df <- df[, id_vars, FALSE]
dates_df[, rsp_var] <- df[, rsp_var, FALSE]
#dates_df <- data.frame(.date=strptime(df[, var], "%Y-%m-%d %H:%M:%S"))
dates_df <- cbind(dates_df, data.frame(.date=strptime(df[, var],
glb_date_fmts[[var]], tz=glb_date_tzs[[var]])))
# print(dates_df[is.na(dates_df$.date), c("ID", "Arrest.fctr", ".date")])
# print(glb_allobs_df[is.na(dates_df$.date), c("ID", "Arrest.fctr", "Date")])
# print(head(glb_allobs_df[grepl("4/7/02 .:..", glb_allobs_df$Date), c("ID", "Arrest.fctr", "Date")]))
# print(head(strptime(glb_allobs_df[grepl("4/7/02 .:..", glb_allobs_df$Date), "Date"], "%m/%e/%y %H:%M"))
# Wrong data during EST->EDT transition
# tmp <- strptime("4/7/02 2:00","%m/%e/%y %H:%M:%S"); print(tmp); print(is.na(tmp))
# dates_df[dates_df$ID == 2068197, .date] <- tmp
# grep("(.*?) 2:(.*)", glb_allobs_df[is.na(dates_df$.date), "Date"], value=TRUE)
# dates_df[is.na(dates_df$.date), ".date"] <-
# data.frame(.date=strptime(gsub("(.*?) 2:(.*)", "\\1 3:\\2",
# glb_allobs_df[is.na(dates_df$.date), "Date"]), "%m/%e/%y %H:%M"))$.date
if (sum(is.na(dates_df$.date)) > 0) {
stop("NA POSIX dates for ", var)
print(df[is.na(dates_df$.date), c(id_vars, rsp_var, var)])
}
.date <- dates_df$.date
dates_df[, paste0(var, ".POSIX")] <- .date
dates_df[, paste0(var, ".year")] <- as.numeric(format(.date, "%Y"))
dates_df[, paste0(var, ".year.fctr")] <- as.factor(format(.date, "%Y"))
dates_df[, paste0(var, ".month")] <- as.numeric(format(.date, "%m"))
dates_df[, paste0(var, ".month.fctr")] <- as.factor(format(.date, "%m"))
dates_df[, paste0(var, ".date")] <- as.numeric(format(.date, "%d"))
dates_df[, paste0(var, ".date.fctr")] <-
cut(as.numeric(format(.date, "%d")), 5) # by month week
dates_df[, paste0(var, ".juliandate")] <- as.numeric(format(.date, "%j"))
# wkday Sun=0; Mon=1; ...; Sat=6
dates_df[, paste0(var, ".wkday")] <- as.numeric(format(.date, "%w"))
dates_df[, paste0(var, ".wkday.fctr")] <- as.factor(format(.date, "%w"))
# Get US Federal Holidays for relevant years
require(XML)
doc.html = htmlTreeParse('http://about.usps.com/news/events-calendar/2012-federal-holidays.htm', useInternal = TRUE)
# # Extract all the paragraphs (HTML tag is p, starting at
# # the root of the document). Unlist flattens the list to
# # create a character vector.
# doc.text = unlist(xpathApply(doc.html, '//p', xmlValue))
# # Replace all \n by spaces
# doc.text = gsub('\\n', ' ', doc.text)
# # Join all the elements of the character vector into a single
# # character string, separated by spaces
# doc.text = paste(doc.text, collapse = ' ')
# parse the tree by tables
txt <- unlist(strsplit(xpathSApply(doc.html, "//*/table", xmlValue), "\n"))
# do some clean up with regular expressions
txt <- grep("day, ", txt, value=TRUE)
txt <- trimws(gsub("(.*?)day, (.*)", "\\2", txt))
# txt <- gsub("\t","",txt)
# txt <- sub("^[[:space:]]*(.*?)[[:space:]]*$", "\\1", txt, perl=TRUE)
# txt <- txt[!(txt %in% c("", "|"))]
hldays <- strptime(paste(txt, ", 2012", sep=""), "%B %e, %Y")
dates_df[, paste0(var, ".hlday")] <-
ifelse(format(.date, "%Y-%m-%d") %in% hldays, 1, 0)
# NYState holidays 1.9., 13.10., 11.11., 27.11., 25.12.
dates_df[, paste0(var, ".wkend")] <- as.numeric(
(dates_df[, paste0(var, ".wkday")] %in% c(0, 6)) |
dates_df[, paste0(var, ".hlday")] )
dates_df[, paste0(var, ".hour")] <- as.numeric(format(.date, "%H"))
dates_df[, paste0(var, ".hour.fctr")] <-
if (length(unique(vals <- as.numeric(format(.date, "%H")))) <= 1)
vals else cut(vals, 3) # by work-shift
dates_df[, paste0(var, ".minute")] <- as.numeric(format(.date, "%M"))
dates_df[, paste0(var, ".minute.fctr")] <-
if (length(unique(vals <- as.numeric(format(.date, "%M")))) <= 1)
vals else cut(vals, 4) # by quarter-hours
dates_df[, paste0(var, ".second")] <- as.numeric(format(.date, "%S"))
dates_df[, paste0(var, ".second.fctr")] <-
if (length(unique(vals <- as.numeric(format(.date, "%S")))) <= 1)
vals else cut(vals, 4) # by quarter-minutes
dates_df[, paste0(var, ".day.minutes")] <-
60 * dates_df[, paste0(var, ".hour")] +
dates_df[, paste0(var, ".minute")]
if ((unq_vals_n <- length(unique(dates_df[, paste0(var, ".day.minutes")]))) > 1) {
max_degree <- min(unq_vals_n, 5)
dates_df[, paste0(var, ".day.minutes.poly.", 1:max_degree)] <-
as.matrix(poly(dates_df[, paste0(var, ".day.minutes")], max_degree))
} else max_degree <- 0
# print(gp <- myplot_box(df=dates_df, ycol_names="PubDate.day.minutes",
# xcol_name=rsp_var))
# print(gp <- myplot_scatter(df=dates_df, xcol_name=".rownames",
# ycol_name="PubDate.day.minutes", colorcol_name=rsp_var))
# print(gp <- myplot_scatter(df=dates_df, xcol_name="PubDate.juliandate",
# ycol_name="PubDate.day.minutes.poly.1", colorcol_name=rsp_var))
# print(gp <- myplot_scatter(df=dates_df, xcol_name="PubDate.day.minutes",
# ycol_name="PubDate.day.minutes.poly.4", colorcol_name=rsp_var))
#
# print(gp <- myplot_scatter(df=dates_df, xcol_name="PubDate.juliandate",
# ycol_name="PubDate.day.minutes", colorcol_name=rsp_var, smooth=TRUE))
# print(gp <- myplot_scatter(df=dates_df, xcol_name="PubDate.juliandate",
# ycol_name="PubDate.day.minutes.poly.4", colorcol_name=rsp_var, smooth=TRUE))
# print(gp <- myplot_scatter(df=dates_df, xcol_name="PubDate.juliandate",
# ycol_name=c("PubDate.day.minutes", "PubDate.day.minutes.poly.4"),
# colorcol_name=rsp_var))
# print(gp <- myplot_scatter(df=subset(dates_df, Popular.fctr=="Y"),
# xcol_name=paste0(var, ".juliandate"),
# ycol_name=paste0(var, ".day.minutes", colorcol_name=rsp_var))
# print(gp <- myplot_box(df=dates_df, ycol_names=paste0(var, ".hour"),
# xcol_name=rsp_var))
# print(gp <- myplot_bar(df=dates_df, ycol_names=paste0(var, ".hour.fctr"),
# xcol_name=rsp_var,
# colorcol_name=paste0(var, ".hour.fctr")))
keep_feats <- paste(var,
c(".POSIX", ".year.fctr", ".month.fctr", ".date.fctr", ".wkday.fctr",
".wkend", ".hour.fctr", ".minute.fctr", ".second.fctr"), sep="")
if (max_degree > 0)
keep_feats <- union(keep_feats, paste(var,
paste0(".day.minutes.poly.", 1:max_degree), sep=""))
keep_feats <- intersect(keep_feats, names(dates_df))
}
#myprint_df(dates_df)
return(dates_df[, keep_feats])
}
if (!is.null(glb_date_vars)) {
glb_allobs_df <- cbind(glb_allobs_df,
myextract_dates_df(df=glb_allobs_df, vars=glb_date_vars,
id_vars=glb_id_var, rsp_var=glb_rsp_var))
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features,
paste(glb_date_vars, c("", ".POSIX"), sep=""))
for (feat in glb_date_vars) {
glb_allobs_df <- orderBy(reformulate(paste0(feat, ".POSIX")), glb_allobs_df)
# print(myplot_scatter(glb_allobs_df, xcol_name=paste0(feat, ".POSIX"),
# ycol_name=glb_rsp_var, colorcol_name=glb_rsp_var))
print(myplot_scatter(glb_allobs_df[glb_allobs_df[, paste0(feat, ".POSIX")] >=
strptime("2012-12-01", "%Y-%m-%d"), ],
xcol_name=paste0(feat, ".POSIX"),
ycol_name=glb_rsp_var, colorcol_name=paste0(feat, ".wkend")))
# Create features that measure the gap between previous timestamp in the data
require(zoo)
z <- zoo(as.numeric(as.POSIXlt(glb_allobs_df[, paste0(feat, ".POSIX")])))
glb_allobs_df[, paste0(feat, ".zoo")] <- z
print(head(glb_allobs_df[, c(glb_id_var, feat, paste0(feat, ".zoo"))]))
print(myplot_scatter(glb_allobs_df[glb_allobs_df[, paste0(feat, ".POSIX")] >
strptime("2012-10-01", "%Y-%m-%d"), ],
xcol_name=paste0(feat, ".zoo"), ycol_name=glb_rsp_var,
colorcol_name=glb_rsp_var))
b <- zoo(, seq(nrow(glb_allobs_df)))
last1 <- as.numeric(merge(z-lag(z, -1), b, all=TRUE)); last1[is.na(last1)] <- 0
glb_allobs_df[, paste0(feat, ".last1.log")] <- log(1 + last1)
print(gp <- myplot_box(df=glb_allobs_df[glb_allobs_df[,
paste0(feat, ".last1.log")] > 0, ],
ycol_names=paste0(feat, ".last1.log"),
xcol_name=glb_rsp_var))
last10 <- as.numeric(merge(z-lag(z, -10), b, all=TRUE)); last10[is.na(last10)] <- 0
glb_allobs_df[, paste0(feat, ".last10.log")] <- log(1 + last10)
print(gp <- myplot_box(df=glb_allobs_df[glb_allobs_df[,
paste0(feat, ".last10.log")] > 0, ],
ycol_names=paste0(feat, ".last10.log"),
xcol_name=glb_rsp_var))
last100 <- as.numeric(merge(z-lag(z, -100), b, all=TRUE)); last100[is.na(last100)] <- 0
glb_allobs_df[, paste0(feat, ".last100.log")] <- log(1 + last100)
print(gp <- myplot_box(df=glb_allobs_df[glb_allobs_df[,
paste0(feat, ".last100.log")] > 0, ],
ycol_names=paste0(feat, ".last100.log"),
xcol_name=glb_rsp_var))
glb_allobs_df <- orderBy(reformulate(glb_id_var), glb_allobs_df)
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features,
c(paste0(feat, ".zoo")))
# all2$last3 = as.numeric(merge(z-lag(z, -3), b, all = TRUE))
# all2$last5 = as.numeric(merge(z-lag(z, -5), b, all = TRUE))
# all2$last10 = as.numeric(merge(z-lag(z, -10), b, all = TRUE))
# all2$last20 = as.numeric(merge(z-lag(z, -20), b, all = TRUE))
# all2$last50 = as.numeric(merge(z-lag(z, -50), b, all = TRUE))
#
#
# # order table
# all2 = all2[order(all2$id),]
#
# ## fill in NAs
# # count averages
# na.avg = all2 %>% group_by(weekend, hour) %>% dplyr::summarise(
# last1=mean(last1, na.rm=TRUE),
# last3=mean(last3, na.rm=TRUE),
# last5=mean(last5, na.rm=TRUE),
# last10=mean(last10, na.rm=TRUE),
# last20=mean(last20, na.rm=TRUE),
# last50=mean(last50, na.rm=TRUE)
# )
#
# # fill in averages
# na.merge = merge(all2, na.avg, by=c("weekend","hour"))
# na.merge = na.merge[order(na.merge$id),]
# for(i in c("last1", "last3", "last5", "last10", "last20", "last50")) {
# y = paste0(i, ".y")
# idx = is.na(all2[[i]])
# all2[idx,][[i]] <- na.merge[idx,][[y]]
# }
# rm(na.avg, na.merge, b, i, idx, n, pd, sec, sh, y, z)
}
}
# check distribution of all numeric data
dsp_numeric_feats_dstrb <- function(feats_vctr) {
for (feat in feats_vctr) {
print(sprintf("feat: %s", feat))
if (glb_is_regression)
gp <- myplot_scatter(df=glb_allobs_df, ycol_name=glb_rsp_var, xcol_name=feat,
smooth=TRUE)
if (glb_is_classification)
gp <- myplot_box(df=glb_allobs_df, ycol_names=feat, xcol_name=glb_rsp_var)
if (inherits(glb_allobs_df[, feat], "factor"))
gp <- gp + facet_wrap(reformulate(feat))
print(gp)
}
}
# dsp_numeric_vars_dstrb(setdiff(names(glb_allobs_df),
# union(myfind_chr_cols_df(glb_allobs_df),
# c(glb_rsp_var_raw, glb_rsp_var))))
add_new_diag_feats <- function(obs_df, ref_df=glb_allobs_df) {
require(plyr)
obs_df <- mutate(obs_df,
# <col_name>.NA=is.na(<col_name>),
# <col_name>.fctr=factor(<col_name>,
# as.factor(union(obs_df$<col_name>, obs_twin_df$<col_name>))),
# <col_name>.fctr=relevel(factor(<col_name>,
# as.factor(union(obs_df$<col_name>, obs_twin_df$<col_name>))),
# "<ref_val>"),
# <col2_name>.fctr=relevel(factor(ifelse(<col1_name> == <val>, "<oth_val>", "<ref_val>")),
# as.factor(c("R", "<ref_val>")),
# ref="<ref_val>"),
# This doesn't work - use sapply instead
# <col_name>.fctr_num=grep(<col_name>, levels(<col_name>.fctr)),
#
# Date.my=as.Date(strptime(Date, "%m/%d/%y %H:%M")),
# Year=year(Date.my),
# Month=months(Date.my),
# Weekday=weekdays(Date.my)
# <col_name>=<table>[as.character(<col2_name>)],
# <col_name>=as.numeric(<col2_name>),
# <col_name> = trunc(<col2_name> / 100),
.rnorm = rnorm(n=nrow(obs_df))
)
# If levels of a factor are different across obs_df & glb_newobs_df; predict.glm fails
# Transformations not handled by mutate
# obs_df$<col_name>.fctr.num <- sapply(1:nrow(obs_df),
# function(row_ix) grep(obs_df[row_ix, "<col_name>"],
# levels(obs_df[row_ix, "<col_name>.fctr"])))
#print(summary(obs_df))
#print(sapply(names(obs_df), function(col) sum(is.na(obs_df[, col]))))
return(obs_df)
}
glb_allobs_df <- add_new_diag_feats(glb_allobs_df)## Loading required package: plyrrequire(dplyr)## Loading required package: dplyr
##
## Attaching package: 'dplyr'
##
## The following objects are masked from 'package:plyr':
##
## arrange, count, desc, failwith, id, mutate, rename, summarise,
## summarize
##
## The following object is masked from 'package:stats':
##
## filter
##
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union#stop(here"); sav_allobs_df <- glb_allobs_df # glb_allobs_df <- sav_allobs_df
# Merge some <descriptor>
# glb_allobs_df$<descriptor>.my <- glb_allobs_df$<descriptor>
# glb_allobs_df[grepl("\\bAIRPORT\\b", glb_allobs_df$<descriptor>.my),
# "<descriptor>.my"] <- "AIRPORT"
# glb_allobs_df$<descriptor>.my <-
# plyr::revalue(glb_allobs_df$<descriptor>.my, c(
# "ABANDONED BUILDING" = "OTHER",
# "##" = "##"
# ))
# print(<descriptor>_freq_df <- mycreate_sqlxtab_df(glb_allobs_df, c("<descriptor>.my")))
# # print(dplyr::filter(<descriptor>_freq_df, grepl("(MEDICAL|DENTAL|OFFICE)", <descriptor>.my)))
# # print(dplyr::filter(dplyr::select(glb_allobs_df, -<var.zoo>),
# # grepl("STORE", <descriptor>.my)))
# glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features, "<descriptor>")
# Check distributions of newly transformed / extracted vars
# Enhancement: remove vars that were displayed ealier
dsp_numeric_feats_dstrb(feats_vctr=setdiff(names(glb_allobs_df),
c(myfind_chr_cols_df(glb_allobs_df), glb_rsp_var_raw, glb_rsp_var,
glb_exclude_vars_as_features)))## [1] "feat: Internet.Use"## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## [1] "feat: Smartphone"## Warning in loop_apply(n, do.ply): Removed 235 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 235 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 235 rows containing missing
## values (geom_point).
## [1] "feat: Age"## Warning in loop_apply(n, do.ply): Removed 237 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 237 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 237 rows containing missing
## values (geom_point).
## [1] "feat: Conservativeness"## Warning in loop_apply(n, do.ply): Removed 259 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 259 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 259 rows containing missing
## values (geom_point).
## [1] "feat: Info.On.Internet"## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## [1] "feat: Worry.About.Info"## Warning in loop_apply(n, do.ply): Removed 217 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 217 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 217 rows containing missing
## values (geom_point).
## [1] "feat: Anonymity.Possible"## Warning in loop_apply(n, do.ply): Removed 254 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 254 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 254 rows containing missing
## values (geom_point).
## [1] "feat: Tried.Masking.Identity"## Warning in loop_apply(n, do.ply): Removed 223 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 223 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 223 rows containing missing
## values (geom_point).
## [1] "feat: Privacy.Laws.Effective"## Warning in loop_apply(n, do.ply): Removed 279 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 279 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 279 rows containing missing
## values (geom_point).
## [1] "feat: .rnorm"## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
# Convert factors to dummy variables
# Build splines require(splines); bsBasis <- bs(training$age, df=3)
#pairs(subset(glb_trnobs_df, select=-c(col_symbol)))
# Check for glb_newobs_df & glb_trnobs_df features range mismatches
# Other diagnostics:
# print(subset(glb_trnobs_df, <col1_name> == max(glb_trnobs_df$<col1_name>, na.rm=TRUE) &
# <col2_name> <= mean(glb_trnobs_df$<col1_name>, na.rm=TRUE)))
# print(glb_trnobs_df[which.max(glb_trnobs_df$<col_name>),])
# print(<col_name>_freq_glb_trnobs_df <- mycreate_tbl_df(glb_trnobs_df, "<col_name>"))
# print(which.min(table(glb_trnobs_df$<col_name>)))
# print(which.max(table(glb_trnobs_df$<col_name>)))
# print(which.max(table(glb_trnobs_df$<col1_name>, glb_trnobs_df$<col2_name>)[, 2]))
# print(table(glb_trnobs_df$<col1_name>, glb_trnobs_df$<col2_name>))
# print(table(is.na(glb_trnobs_df$<col1_name>), glb_trnobs_df$<col2_name>))
# print(table(sign(glb_trnobs_df$<col1_name>), glb_trnobs_df$<col2_name>))
# print(mycreate_xtab_df(glb_trnobs_df, <col1_name>))
# print(mycreate_xtab_df(glb_trnobs_df, c(<col1_name>, <col2_name>)))
# print(<col1_name>_<col2_name>_xtab_glb_trnobs_df <-
# mycreate_xtab_df(glb_trnobs_df, c("<col1_name>", "<col2_name>")))
# <col1_name>_<col2_name>_xtab_glb_trnobs_df[is.na(<col1_name>_<col2_name>_xtab_glb_trnobs_df)] <- 0
# print(<col1_name>_<col2_name>_xtab_glb_trnobs_df <-
# mutate(<col1_name>_<col2_name>_xtab_glb_trnobs_df,
# <col3_name>=(<col1_name> * 1.0) / (<col1_name> + <col2_name>)))
# print(mycreate_sqlxtab_df(glb_allobs_df, c("<col1_name>", "<col2_name>")))
# print(<col2_name>_min_entity_arr <-
# sort(tapply(glb_trnobs_df$<col1_name>, glb_trnobs_df$<col2_name>, min, na.rm=TRUE)))
# print(<col1_name>_na_by_<col2_name>_arr <-
# sort(tapply(glb_trnobs_df$<col1_name>.NA, glb_trnobs_df$<col2_name>, mean, na.rm=TRUE)))
# Other plots:
# print(myplot_box(df=glb_trnobs_df, ycol_names="<col1_name>"))
# print(myplot_box(df=glb_trnobs_df, ycol_names="<col1_name>", xcol_name="<col2_name>"))
# print(myplot_line(subset(glb_trnobs_df, Symbol %in% c("CocaCola", "ProcterGamble")),
# "Date.POSIX", "StockPrice", facet_row_colnames="Symbol") +
# geom_vline(xintercept=as.numeric(as.POSIXlt("2003-03-01"))) +
# geom_vline(xintercept=as.numeric(as.POSIXlt("1983-01-01")))
# )
# print(myplot_line(subset(glb_trnobs_df, Date.POSIX > as.POSIXct("2004-01-01")),
# "Date.POSIX", "StockPrice") +
# geom_line(aes(color=Symbol)) +
# coord_cartesian(xlim=c(as.POSIXct("1990-01-01"),
# as.POSIXct("2000-01-01"))) +
# coord_cartesian(ylim=c(0, 250)) +
# geom_vline(xintercept=as.numeric(as.POSIXlt("1997-09-01"))) +
# geom_vline(xintercept=as.numeric(as.POSIXlt("1997-11-01")))
# )
# print(myplot_scatter(glb_allobs_df, "<col1_name>", "<col2_name>", smooth=TRUE))
# print(myplot_scatter(glb_allobs_df, "<col1_name>", "<col2_name>", colorcol_name="<Pred.fctr>") +
# geom_point(data=subset(glb_allobs_df, <condition>),
# mapping=aes(x=<x_var>, y=<y_var>), color="red", shape=4, size=5))
rm(srt_allobs_df, last1, last10, last100, pd)## Warning in rm(srt_allobs_df, last1, last10, last100, pd): object
## 'srt_allobs_df' not found## Warning in rm(srt_allobs_df, last1, last10, last100, pd): object 'last1'
## not found## Warning in rm(srt_allobs_df, last1, last10, last100, pd): object 'last10'
## not found## Warning in rm(srt_allobs_df, last1, last10, last100, pd): object 'last100'
## not found## Warning in rm(srt_allobs_df, last1, last10, last100, pd): object 'pd' not
## foundglb_chunks_df <- myadd_chunk(glb_chunks_df, "scrub.data", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 2 inspect.data 2 0 9.966 15.619 5.653
## 3 scrub.data 2 1 15.620 NA NAStep 2.1: scrub data
# Options:
# 1. Not fill missing vars
# 2. Fill missing numerics with a different algorithm
# 3. Fill missing chars with data based on clusters
mycheck_problem_data(glb_allobs_df)## [1] "numeric data missing in glb_allobs_df: "
## Internet.Use Smartphone Age
## 1 43 27
## Conservativeness Info.On.Internet Worry.About.Info
## 62 210 212
## Privacy.Importance Anonymity.Possible Tried.Masking.Identity
## 215 249 218
## Privacy.Laws.Effective
## 108
## [1] "numeric data w/ 0s in glb_allobs_df: "
## Internet.Use Smartphone Info.On.Internet
## 226 472 105
## Worry.About.Info Privacy.Importance Anonymity.Possible
## 404 43 475
## Tried.Masking.Identity Privacy.Laws.Effective
## 656 660
## [1] "numeric data w/ Infs in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ NaNs in glb_allobs_df: "
## named integer(0)
## [1] "string data missing in glb_allobs_df: "
## Sex State Region .rownames
## 0 0 0 0# if (!is.null(glb_force_0_to_NA_vars)) {
# for (feat in glb_force_0_to_NA_vars) {
# warning("Forcing ", sum(glb_allobs_df[, feat] == 0),
# " obs with ", feat, " 0s to NAs")
# glb_allobs_df[glb_allobs_df[, feat] == 0, feat] <- NA
# }
# }
mycheck_problem_data(glb_allobs_df)## [1] "numeric data missing in glb_allobs_df: "
## Internet.Use Smartphone Age
## 1 43 27
## Conservativeness Info.On.Internet Worry.About.Info
## 62 210 212
## Privacy.Importance Anonymity.Possible Tried.Masking.Identity
## 215 249 218
## Privacy.Laws.Effective
## 108
## [1] "numeric data w/ 0s in glb_allobs_df: "
## Internet.Use Smartphone Info.On.Internet
## 226 472 105
## Worry.About.Info Privacy.Importance Anonymity.Possible
## 404 43 475
## Tried.Masking.Identity Privacy.Laws.Effective
## 656 660
## [1] "numeric data w/ Infs in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ NaNs in glb_allobs_df: "
## named integer(0)
## [1] "string data missing in glb_allobs_df: "
## Sex State Region .rownames
## 0 0 0 0dsp_catgs <- function() {
print("NewsDesk:")
print(table(glb_allobs_df$NewsDesk))
print("SectionName:")
print(table(glb_allobs_df$SectionName))
print("SubsectionName:")
print(table(glb_allobs_df$SubsectionName))
}
# sel_obs <- function(Popular=NULL,
# NewsDesk=NULL, SectionName=NULL, SubsectionName=NULL,
# Headline.contains=NULL, Snippet.contains=NULL, Abstract.contains=NULL,
# Headline.pfx=NULL, NewsDesk.nb=NULL, .clusterid=NULL, myCategory=NULL,
# perl=FALSE) {
sel_obs <- function(vars_lst) {
tmp_df <- glb_allobs_df
# Does not work for Popular == NAs ???
if (!is.null(Popular)) {
if (is.na(Popular))
tmp_df <- tmp_df[is.na(tmp_df$Popular), ] else
tmp_df <- tmp_df[tmp_df$Popular == Popular, ]
}
if (!is.null(NewsDesk))
tmp_df <- tmp_df[tmp_df$NewsDesk == NewsDesk, ]
if (!is.null(SectionName))
tmp_df <- tmp_df[tmp_df$SectionName == SectionName, ]
if (!is.null(SubsectionName))
tmp_df <- tmp_df[tmp_df$SubsectionName == SubsectionName, ]
if (!is.null(Headline.contains))
tmp_df <-
tmp_df[grep(Headline.contains, tmp_df$Headline, perl=perl), ]
if (!is.null(Snippet.contains))
tmp_df <-
tmp_df[grep(Snippet.contains, tmp_df$Snippet, perl=perl), ]
if (!is.null(Abstract.contains))
tmp_df <-
tmp_df[grep(Abstract.contains, tmp_df$Abstract, perl=perl), ]
if (!is.null(Headline.pfx)) {
if (length(grep("Headline.pfx", names(tmp_df), fixed=TRUE, value=TRUE))
> 0) tmp_df <-
tmp_df[tmp_df$Headline.pfx == Headline.pfx, ] else
warning("glb_allobs_df does not contain Headline.pfx; ignoring that filter")
}
if (!is.null(NewsDesk.nb)) {
if (any(grepl("NewsDesk.nb", names(tmp_df), fixed=TRUE)) > 0)
tmp_df <-
tmp_df[tmp_df$NewsDesk.nb == NewsDesk.nb, ] else
warning("glb_allobs_df does not contain NewsDesk.nb; ignoring that filter")
}
if (!is.null(.clusterid)) {
if (any(grepl(".clusterid", names(tmp_df), fixed=TRUE)) > 0)
tmp_df <-
tmp_df[tmp_df$clusterid == clusterid, ] else
warning("glb_allobs_df does not contain clusterid; ignoring that filter") }
if (!is.null(myCategory)) {
if (!(myCategory %in% names(glb_allobs_df)))
tmp_df <-
tmp_df[tmp_df$myCategory == myCategory, ] else
warning("glb_allobs_df does not contain myCategory; ignoring that filter")
}
return(glb_allobs_df$UniqueID %in% tmp_df$UniqueID)
}
dsp_obs <- function(..., cols=c(NULL), all=FALSE) {
tmp_df <- glb_allobs_df[sel_obs(...),
union(c("UniqueID", "Popular", "myCategory", "Headline"), cols), FALSE]
if(all) { print(tmp_df) } else { myprint_df(tmp_df) }
}
#dsp_obs(Popular=1, NewsDesk="", SectionName="", Headline.contains="Boehner")
# dsp_obs(Popular=1, NewsDesk="", SectionName="")
# dsp_obs(Popular=NA, NewsDesk="", SectionName="")
dsp_tbl <- function(...) {
tmp_entity_df <- glb_allobs_df[sel_obs(...), ]
tmp_tbl <- table(tmp_entity_df$NewsDesk,
tmp_entity_df$SectionName,
tmp_entity_df$SubsectionName,
tmp_entity_df$Popular, useNA="ifany")
#print(names(tmp_tbl))
#print(dimnames(tmp_tbl))
print(tmp_tbl)
}
dsp_hdlxtab <- function(str)
print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains=str), ],
c("Headline.pfx", "Headline", glb_rsp_var)))
#dsp_hdlxtab("(1914)|(1939)")
dsp_catxtab <- function(str)
print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains=str), ],
c("Headline.pfx", "NewsDesk", "SectionName", "SubsectionName", glb_rsp_var)))
# dsp_catxtab("1914)|(1939)")
# dsp_catxtab("19(14|39|64):")
# dsp_catxtab("19..:")
# Create myCategory <- NewsDesk#SectionName#SubsectionName
# Fix some data before merging categories
# glb_allobs_df[sel_obs(Headline.contains="Your Turn:", NewsDesk=""),
# "NewsDesk"] <- "Styles"
# glb_allobs_df[sel_obs(Headline.contains="School", NewsDesk="", SectionName="U.S.",
# SubsectionName=""),
# "SubsectionName"] <- "Education"
# glb_allobs_df[sel_obs(Headline.contains="Today in Small Business:", NewsDesk="Business"),
# "SectionName"] <- "Business Day"
# glb_allobs_df[sel_obs(Headline.contains="Today in Small Business:", NewsDesk="Business"),
# "SubsectionName"] <- "Small Business"
# glb_allobs_df[sel_obs(Headline.contains="Readers Respond:"),
# "SectionName"] <- "Opinion"
# glb_allobs_df[sel_obs(Headline.contains="Readers Respond:"),
# "SubsectionName"] <- "Room For Debate"
# glb_allobs_df[sel_obs(NewsDesk="Business", SectionName="", SubsectionName="", Popular=NA),
# "SubsectionName"] <- "Small Business"
# print(glb_allobs_df[glb_allobs_df$UniqueID %in% c(7973),
# c("UniqueID", "Headline", "myCategory", "NewsDesk", "SectionName", "SubsectionName")])
#
# glb_allobs_df[sel_obs(NewsDesk="Business", SectionName="", SubsectionName=""),
# "SectionName"] <- "Technology"
# print(glb_allobs_df[glb_allobs_df$UniqueID %in% c(5076, 5736, 5924, 5911, 6532),
# c("UniqueID", "Headline", "myCategory", "NewsDesk", "SectionName", "SubsectionName")])
#
# glb_allobs_df[sel_obs(SectionName="Health"),
# "NewsDesk"] <- "Science"
# glb_allobs_df[sel_obs(SectionName="Travel"),
# "NewsDesk"] <- "Travel"
#
# glb_allobs_df[sel_obs(SubsectionName="Fashion & Style"),
# "SectionName"] <- ""
# glb_allobs_df[sel_obs(SubsectionName="Fashion & Style"),
# "SubsectionName"] <- ""
# glb_allobs_df[sel_obs(NewsDesk="Styles", SectionName="", SubsectionName="", Popular=1),
# "SectionName"] <- "U.S."
# print(glb_allobs_df[glb_allobs_df$UniqueID %in% c(5486),
# c("UniqueID", "Headline", "myCategory", "NewsDesk", "SectionName", "SubsectionName")])
#
# glb_allobs_df$myCategory <- paste(glb_allobs_df$NewsDesk,
# glb_allobs_df$SectionName,
# glb_allobs_df$SubsectionName,
# sep="#")
# dsp_obs( Headline.contains="Music:"
# #,NewsDesk=""
# #,SectionName=""
# #,SubsectionName="Fashion & Style"
# #,Popular=1 #NA
# ,cols= c("UniqueID", "Headline", "Popular", "myCategory",
# "NewsDesk", "SectionName", "SubsectionName"),
# all=TRUE)
# dsp_obs( Headline.contains="."
# ,NewsDesk=""
# ,SectionName="Opinion"
# ,SubsectionName=""
# #,Popular=1 #NA
# ,cols= c("UniqueID", "Headline", "Popular", "myCategory",
# "NewsDesk", "SectionName", "SubsectionName"),
# all=TRUE)
# Merge some categories
# glb_allobs_df$myCategory <-
# plyr::revalue(glb_allobs_df$myCategory, c(
# "#Business Day#Dealbook" = "Business#Business Day#Dealbook",
# "#Business Day#Small Business" = "Business#Business Day#Small Business",
# "#Crosswords/Games#" = "Business#Crosswords/Games#",
# "Business##" = "Business#Technology#",
# "#Open#" = "Business#Technology#",
# "#Technology#" = "Business#Technology#",
#
# "#Arts#" = "Culture#Arts#",
# "Culture##" = "Culture#Arts#",
#
# "#World#Asia Pacific" = "Foreign#World#Asia Pacific",
# "Foreign##" = "Foreign#World#",
#
# "#N.Y. / Region#" = "Metro#N.Y. / Region#",
#
# "#Opinion#" = "OpEd#Opinion#",
# "OpEd##" = "OpEd#Opinion#",
#
# "#Health#" = "Science#Health#",
# "Science##" = "Science#Health#",
#
# "Styles##" = "Styles##Fashion",
# "Styles#Health#" = "Science#Health#",
# "Styles#Style#Fashion & Style" = "Styles##Fashion",
#
# "#Travel#" = "Travel#Travel#",
#
# "Magazine#Magazine#" = "myOther",
# "National##" = "myOther",
# "National#U.S.#Politics" = "myOther",
# "Sports##" = "myOther",
# "Sports#Sports#" = "myOther",
# "#U.S.#" = "myOther",
#
#
# # "Business##Small Business" = "Business#Business Day#Small Business",
# #
# # "#Opinion#" = "#Opinion#Room For Debate",
# "##" = "##"
# # "Business##" = "Business#Business Day#Dealbook",
# # "Foreign#World#" = "Foreign##",
# # "#Open#" = "Other",
# # "#Opinion#The Public Editor" = "OpEd#Opinion#",
# # "Styles#Health#" = "Styles##",
# # "Styles#Style#Fashion & Style" = "Styles##",
# # "#U.S.#" = "#U.S.#Education",
# ))
# ctgry_xtab_df <- orderBy(reformulate(c("-", ".n")),
# mycreate_sqlxtab_df(glb_allobs_df,
# c("myCategory", "NewsDesk", "SectionName", "SubsectionName", glb_rsp_var)))
# myprint_df(ctgry_xtab_df)
# write.table(ctgry_xtab_df, paste0(glb_out_pfx, "ctgry_xtab.csv"),
# row.names=FALSE)
# ctgry_cast_df <- orderBy(~ -Y -NA, dcast(ctgry_xtab_df,
# myCategory + NewsDesk + SectionName + SubsectionName ~
# Popular.fctr, sum, value.var=".n"))
# myprint_df(ctgry_cast_df)
# write.table(ctgry_cast_df, paste0(glb_out_pfx, "ctgry_cast.csv"),
# row.names=FALSE)
# print(ctgry_sum_tbl <- table(glb_allobs_df$myCategory, glb_allobs_df[, glb_rsp_var],
# useNA="ifany"))
dsp_chisq.test <- function(...) {
sel_df <- glb_allobs_df[sel_obs(...) &
!is.na(glb_allobs_df$Popular), ]
sel_df$.marker <- 1
ref_df <- glb_allobs_df[!is.na(glb_allobs_df$Popular), ]
mrg_df <- merge(ref_df[, c(glb_id_var, "Popular")],
sel_df[, c(glb_id_var, ".marker")], all.x=TRUE)
mrg_df[is.na(mrg_df)] <- 0
print(mrg_tbl <- table(mrg_df$.marker, mrg_df$Popular))
print("Rows:Selected; Cols:Popular")
#print(mrg_tbl)
print(chisq.test(mrg_tbl))
}
# dsp_chisq.test(Headline.contains="[Ee]bola")
# dsp_chisq.test(Snippet.contains="[Ee]bola")
# dsp_chisq.test(Abstract.contains="[Ee]bola")
# print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains="[Ee]bola"), ],
# c(glb_rsp_var, "NewsDesk", "SectionName", "SubsectionName")))
# print(table(glb_allobs_df$NewsDesk, glb_allobs_df$SectionName))
# print(table(glb_allobs_df$SectionName, glb_allobs_df$SubsectionName))
# print(table(glb_allobs_df$NewsDesk, glb_allobs_df$SectionName, glb_allobs_df$SubsectionName))
# glb_allobs_df$myCategory.fctr <- as.factor(glb_allobs_df$myCategory)
# glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features,
# c("myCategory", "NewsDesk", "SectionName", "SubsectionName"))
# Copy Headline into Snipper & Abstract if they are empty
# print(glb_allobs_df[nchar(glb_allobs_df[, "Snippet"]) == 0, c("Headline", "Snippet")])
# print(glb_allobs_df[glb_allobs_df$Headline == glb_allobs_df$Snippet,
# c("UniqueID", "Headline", "Snippet")])
# glb_allobs_df[nchar(glb_allobs_df[, "Snippet"]) == 0, "Snippet"] <-
# glb_allobs_df[nchar(glb_allobs_df[, "Snippet"]) == 0, "Headline"]
#
# print(glb_allobs_df[nchar(glb_allobs_df[, "Abstract"]) == 0, c("Headline", "Abstract")])
# print(glb_allobs_df[glb_allobs_df$Headline == glb_allobs_df$Abstract,
# c("UniqueID", "Headline", "Abstract")])
# glb_allobs_df[nchar(glb_allobs_df[, "Abstract"]) == 0, "Abstract"] <-
# glb_allobs_df[nchar(glb_allobs_df[, "Abstract"]) == 0, "Headline"]
# WordCount_0_df <- subset(glb_allobs_df, WordCount == 0)
# table(WordCount_0_df$Popular, WordCount_0_df$WordCount, useNA="ifany")
# myprint_df(WordCount_0_df[,
# c("UniqueID", "Popular", "WordCount", "Headline")])Step 2.1: scrub data
glb_chunks_df <- myadd_chunk(glb_chunks_df, "transform.data", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 3 scrub.data 2 1 15.62 17.419 1.799
## 4 transform.data 2 2 17.42 NA NA### Mapping dictionary
#sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
if (!is.null(glb_map_vars)) {
for (feat in glb_map_vars) {
map_df <- myimport_data(url=glb_map_urls[[feat]],
comment="map_df",
print_diagn=TRUE)
glb_allobs_df <- mymap_codes(glb_allobs_df, feat, names(map_df)[2],
map_df, map_join_col_name=names(map_df)[1],
map_tgt_col_name=names(map_df)[2])
}
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, glb_map_vars)
}
### Forced Assignments
#stop(here"); sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
for (feat in glb_assign_vars) {
new_feat <- paste0(feat, ".my")
print(sprintf("Forced Assignments for: %s -> %s...", feat, new_feat))
glb_allobs_df[, new_feat] <- glb_allobs_df[, feat]
pairs <- glb_assign_pairs_lst[[feat]]
for (pair_ix in 1:length(pairs$from)) {
if (is.na(pairs$from[pair_ix]))
nobs <- nrow(filter(glb_allobs_df,
is.na(eval(parse(text=feat),
envir=glb_allobs_df)))) else
nobs <- sum(glb_allobs_df[, feat] == pairs$from[pair_ix])
#nobs <- nrow(filter(glb_allobs_df, is.na(Married.fctr))) ; print(nobs)
if ((is.na(pairs$from[pair_ix])) && (is.na(pairs$to[pair_ix])))
stop("what are you trying to do ???")
if (is.na(pairs$from[pair_ix]))
glb_allobs_df[is.na(glb_allobs_df[, feat]), new_feat] <-
pairs$to[pair_ix] else
glb_allobs_df[glb_allobs_df[, feat] == pairs$from[pair_ix], new_feat] <-
pairs$to[pair_ix]
print(sprintf(" %s -> %s for %s obs",
pairs$from[pair_ix], pairs$to[pair_ix], format(nobs, big.mark=",")))
}
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, glb_assign_vars)
}## [1] "Forced Assignments for: Internet.Use -> Internet.Use.my..."
## [1] " NA -> 0 for 1 obs"### Transformations using mapping functions
#stop(here"); sav_allobs_df <- glb_allobs_df; glb_allobs_df <- sav_allobs_df
for (feat in glb_transform_vars) {
new_feat <- paste0(feat, glb_transform_lst[[feat]]$sfx)
print(sprintf("Applying mapping function for: %s -> %s...", feat, new_feat))
glb_allobs_df[, new_feat] <- glb_transform_lst[[feat]]$mapfn(glb_allobs_df[, feat])
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, glb_transform_vars)
}## [1] "Applying mapping function for: Age -> Age.my.fctr..."
## [1] "Applying mapping function for: Anonymity.Possible -> Anonymity.Possible.my.fctr..."
## [1] "Applying mapping function for: Conservativeness -> Conservativeness.my.fctr..."
## [1] "Applying mapping function for: Info.On.Internet -> Info.On.Internet.my.fctr..."
## [1] "Applying mapping function for: Privacy.Laws.Effective -> Privacy.Laws.Effective.my.fctr..."
## [1] "Applying mapping function for: Smartphone -> Smartphone.my.fctr..."
## [1] "Applying mapping function for: Tried.Masking.Identity -> Tried.Masking.Identity.my.fctr..."
## [1] "Applying mapping function for: Worry.About.Info -> Worry.About.Info.my.fctr..."Step 2.2: transform data
glb_chunks_df <- myadd_chunk(glb_chunks_df, "manage.missing.data", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 4 transform.data 2 2 17.420 17.556 0.136
## 5 manage.missing.data 2 3 17.556 NA NA# print(sapply(names(glb_trnobs_df), function(col) sum(is.na(glb_trnobs_df[, col]))))
# print(sapply(names(glb_newobs_df), function(col) sum(is.na(glb_newobs_df[, col]))))
# glb_trnobs_df <- na.omit(glb_trnobs_df)
# glb_newobs_df <- na.omit(glb_newobs_df)
# df[is.na(df)] <- 0
mycheck_problem_data(glb_allobs_df)## [1] "numeric data missing in glb_allobs_df: "
## Internet.Use Smartphone Age
## 1 43 27
## Conservativeness Info.On.Internet Worry.About.Info
## 62 210 212
## Privacy.Importance Anonymity.Possible Tried.Masking.Identity
## 215 249 218
## Privacy.Laws.Effective
## 108
## [1] "numeric data w/ 0s in glb_allobs_df: "
## Internet.Use Smartphone
## 226 472
## Info.On.Internet Worry.About.Info
## 105 404
## Privacy.Importance Anonymity.Possible
## 43 475
## Tried.Masking.Identity Privacy.Laws.Effective
## 656 660
## Internet.Use.my Anonymity.Possible.my.fctr
## 227 475
## Info.On.Internet.my.fctr Privacy.Laws.Effective.my.fctr
## 105 660
## Smartphone.my.fctr Tried.Masking.Identity.my.fctr
## 472 656
## Worry.About.Info.my.fctr
## 404
## [1] "numeric data w/ Infs in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ NaNs in glb_allobs_df: "
## named integer(0)
## [1] "string data missing in glb_allobs_df: "
## Sex State Region .rownames
## 0 0 0 0# Not refactored into mydsutils.R since glb_*_df might be reassigned
glb_impute_missing_data <- function() {
require(mice)
set.seed(glb_mice_complete.seed)
inp_impent_df <- glb_allobs_df[, setdiff(names(glb_allobs_df),
union(glb_exclude_vars_as_features, glb_rsp_var))]
print("Summary before imputation: ")
print(summary(inp_impent_df))
out_impent_df <- complete(mice(inp_impent_df))
print(summary(out_impent_df))
# complete(mice()) changes attributes of factors even though values don't change
ret_vars <- sapply(names(out_impent_df),
function(col) ifelse(!identical(out_impent_df[, col], inp_impent_df[, col]),
col, ""))
ret_vars <- ret_vars[ret_vars != ""]
return(out_impent_df[, ret_vars])
}
if (glb_impute_na_data &&
(length(myfind_numerics_missing(glb_allobs_df)) > 0) &&
(ncol(nonna_df <- glb_impute_missing_data()) > 0)) {
for (col in names(nonna_df)) {
glb_allobs_df[, paste0(col, ".nonNA")] <- nonna_df[, col]
glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features, col)
}
}
mycheck_problem_data(glb_allobs_df, terminate = TRUE)## [1] "numeric data missing in glb_allobs_df: "
## Internet.Use Smartphone Age
## 1 43 27
## Conservativeness Info.On.Internet Worry.About.Info
## 62 210 212
## Privacy.Importance Anonymity.Possible Tried.Masking.Identity
## 215 249 218
## Privacy.Laws.Effective
## 108
## [1] "numeric data w/ 0s in glb_allobs_df: "
## Internet.Use Smartphone
## 226 472
## Info.On.Internet Worry.About.Info
## 105 404
## Privacy.Importance Anonymity.Possible
## 43 475
## Tried.Masking.Identity Privacy.Laws.Effective
## 656 660
## Internet.Use.my Anonymity.Possible.my.fctr
## 227 475
## Info.On.Internet.my.fctr Privacy.Laws.Effective.my.fctr
## 105 660
## Smartphone.my.fctr Tried.Masking.Identity.my.fctr
## 472 656
## Worry.About.Info.my.fctr
## 404
## [1] "numeric data w/ Infs in glb_allobs_df: "
## named integer(0)
## [1] "numeric data w/ NaNs in glb_allobs_df: "
## named integer(0)
## [1] "string data missing in glb_allobs_df: "
## Sex State Region .rownames
## 0 0 0 0Step 2.3: manage missing data
#```{r extract_features, cache=FALSE, eval=!is.null(glb_txt_vars)}
glb_chunks_df <- myadd_chunk(glb_chunks_df, "extract.features", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 5 manage.missing.data 2 3 17.556 17.639 0.083
## 6 extract.features 3 0 17.639 NA NAextract.features_chunk_df <- myadd_chunk(NULL, "extract.features_bgn")## label step_major step_minor bgn end elapsed
## 1 extract.features_bgn 1 0 17.645 NA NA# Options:
# Select Tf, log(1 + Tf), Tf-IDF or BM25Tf-IDf
# Create new features that help prediction
# <col_name>.lag.2 <- lag(zoo(glb_trnobs_df$<col_name>), -2, na.pad=TRUE)
# glb_trnobs_df[, "<col_name>.lag.2"] <- coredata(<col_name>.lag.2)
# <col_name>.lag.2 <- lag(zoo(glb_newobs_df$<col_name>), -2, na.pad=TRUE)
# glb_newobs_df[, "<col_name>.lag.2"] <- coredata(<col_name>.lag.2)
#
# glb_newobs_df[1, "<col_name>.lag.2"] <- glb_trnobs_df[nrow(glb_trnobs_df) - 1,
# "<col_name>"]
# glb_newobs_df[2, "<col_name>.lag.2"] <- glb_trnobs_df[nrow(glb_trnobs_df),
# "<col_name>"]
# glb_allobs_df <- mutate(glb_allobs_df,
# A.P.http=ifelse(grepl("http",Added,fixed=TRUE), 1, 0)
# )
#
# glb_trnobs_df <- mutate(glb_trnobs_df,
# )
#
# glb_newobs_df <- mutate(glb_newobs_df,
# )
# Create factors of string variables
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "factorize.str.vars"), major.inc=TRUE)## label step_major step_minor bgn end
## 1 extract.features_bgn 1 0 17.645 17.653
## 2 extract.features_factorize.str.vars 2 0 17.653 NA
## elapsed
## 1 0.008
## 2 NA#stop(here"); sav_allobs_df <- glb_allobs_df; #glb_allobs_df <- sav_allobs_df
print(str_vars <- myfind_chr_cols_df(glb_allobs_df))## Sex State Region .rownames .src
## "Sex" "State" "Region" ".rownames" ".src"if (length(str_vars <- setdiff(str_vars,
glb_exclude_vars_as_features)) > 0) {
for (var in str_vars) {
warning("Creating factors of string variable: ", var,
": # of unique values: ", length(unique(glb_allobs_df[, var])))
glb_allobs_df[, paste0(var, ".fctr")] <- factor(glb_allobs_df[, var],
as.factor(unique(glb_allobs_df[, var])))
# glb_trnobs_df[, paste0(var, ".fctr")] <- factor(glb_trnobs_df[, var],
# as.factor(unique(glb_allobs_df[, var])))
# glb_newobs_df[, paste0(var, ".fctr")] <- factor(glb_newobs_df[, var],
# as.factor(unique(glb_allobs_df[, var])))
}
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features, str_vars)
}## Warning: Creating factors of string variable: Sex: # of unique values: 2## Warning: Creating factors of string variable: State: # of unique values: 49## Warning: Creating factors of string variable: Region: # of unique values: 4if (!is.null(glb_txt_vars)) {
require(foreach)
require(gsubfn)
require(stringr)
require(tm)
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "process.text"), major.inc=TRUE)
chk_pattern_freq <- function(re_str, ignore.case=TRUE) {
match_mtrx <- str_extract_all(txt_vctr, regex(re_str, ignore_case=ignore.case),
simplify=TRUE)
match_df <- as.data.frame(match_mtrx[match_mtrx != ""])
names(match_df) <- "pattern"
return(mycreate_sqlxtab_df(match_df, "pattern"))
}
#tmp_freq_df <- chk_pattern_freq("\\bNew (\\w)+", ignore.case=FALSE)
#subset(chk_pattern_freq("\\bNew (\\w)+", ignore.case=FALSE), grepl("New [[:upper:]]", pattern))
#chk_pattern_freq("\\bnew (\\W)+")
chk_subfn <- function(pos_ix) {
re_str <- gsubfn_args_lst[["re_str"]][[pos_ix]]
print("re_str:"); print(re_str)
rp_frmla <- gsubfn_args_lst[["rp_frmla"]][[pos_ix]]
print("rp_frmla:"); print(rp_frmla, showEnv=FALSE)
tmp_vctr <- grep(re_str, txt_vctr, value=TRUE, ignore.case=TRUE)[1:5]
print("Before:")
print(tmp_vctr)
print("After:")
print(gsubfn(re_str, rp_frmla, tmp_vctr, ignore.case=TRUE))
}
#chk_subfn(1)
myapply_gsub <- function(...) {
if ((length_lst <- length(names(gsub_map_lst))) == 0)
return(txt_vctr)
for (ptn_ix in 1:length_lst) {
print(sprintf("running gsub for %02d (of %02d): #%s#...", ptn_ix,
length(names(gsub_map_lst)), names(gsub_map_lst)[ptn_ix]))
txt_vctr <- gsub(names(gsub_map_lst)[ptn_ix], gsub_map_lst[[ptn_ix]],
txt_vctr, ...)
}
return(txt_vctr)
}
myapply_txtmap <- function(txt_vctr, ...) {
nrows <- nrow(glb_txt_map_df)
for (ptn_ix in 1:nrows) {
print(sprintf("running gsub for %02d (of %02d): #%s#...", ptn_ix,
nrows, glb_txt_map_df[ptn_ix, "rex_str"]))
txt_vctr <- gsub(glb_txt_map_df[ptn_ix, "rex_str"],
glb_txt_map_df[ptn_ix, "rpl_str"],
txt_vctr, ...)
}
return(txt_vctr)
}
chk.equal <- function(bgn, end) {
print(all.equal(sav_txt_lst[["Headline"]][bgn:end], glb_txt_lst[["Headline"]][bgn:end]))
}
dsp.equal <- function(bgn, end) {
print(sav_txt_lst[["Headline"]][bgn:end])
print(glb_txt_lst[["Headline"]][bgn:end])
}
#sav_txt_lst <- glb_txt_lst; all.equal(sav_txt_lst, glb_txt_lst)
#all.equal(sav_txt_lst[["Headline"]][1:4200], glb_txt_lst[["Headline"]][1:4200])
#all.equal(sav_txt_lst[["Headline"]][1:2000], glb_txt_lst[["Headline"]][1:2000])
#all.equal(sav_txt_lst[["Headline"]][1:1000], glb_txt_lst[["Headline"]][1:1000])
#all.equal(sav_txt_lst[["Headline"]][1:500], glb_txt_lst[["Headline"]][1:500])
#all.equal(sav_txt_lst[["Headline"]][1:200], glb_txt_lst[["Headline"]][1:200])
#all.equal(sav_txt_lst[["Headline"]][1:100], glb_txt_lst[["Headline"]][1:100])
#chk.equal( 1, 100)
#chk.equal(51, 100)
#chk.equal(81, 100)
#chk.equal(81, 90)
#chk.equal(81, 85)
#chk.equal(86, 90)
#chk.equal(96, 100)
#dsp.equal(86, 90)
glb_txt_map_df <- read.csv("mytxt_map.csv", comment.char="#", strip.white=TRUE)
glb_txt_lst <- list();
print(sprintf("Building glb_txt_lst..."))
glb_txt_lst <- foreach(txt_var=glb_txt_vars) %dopar% {
# for (txt_var in glb_txt_vars) {
txt_vctr <- glb_allobs_df[, txt_var]
# myapply_txtmap shd be created as a tm_map::content_transformer ?
#print(glb_txt_map_df)
#txt_var=glb_txt_vars[3]; txt_vctr <- glb_txt_lst[[txt_var]]
#print(rex_str <- glb_txt_map_df[glb_txt_map_df$rex_str == "\\bWall St\\.", "rex_str"])
#print(rex_str <- glb_txt_map_df[grepl("du Pont", glb_txt_map_df$rex_str), "rex_str"])
#print(rex_str <- glb_txt_map_df[glb_txt_map_df$rpl_str == "versus", "rex_str"])
#print(tmp_vctr <- grep(rex_str, txt_vctr, value=TRUE, ignore.case=FALSE))
#ret_lst <- regexec(rex_str, txt_vctr, ignore.case=FALSE); ret_lst <- regmatches(txt_vctr, ret_lst); ret_vctr <- sapply(1:length(ret_lst), function(pos_ix) ifelse(length(ret_lst[[pos_ix]]) > 0, ret_lst[[pos_ix]], "")); print(ret_vctr <- ret_vctr[ret_vctr != ""])
#gsub(rex_str, glb_txt_map_df[glb_txt_map_df$rex_str == rex_str, "rpl_str"], tmp_vctr, ignore.case=FALSE)
#grep("Hong Hong", txt_vctr, value=TRUE)
txt_vctr <- myapply_txtmap(txt_vctr, ignore.case=FALSE)
}
names(glb_txt_lst) <- glb_txt_vars
for (txt_var in glb_txt_vars) {
print(sprintf("Remaining Acronyms in %s:", txt_var))
txt_vctr <- glb_txt_lst[[txt_var]]
print(tmp_vctr <- grep("[[:upper:]]\\.", txt_vctr, value=TRUE, ignore.case=FALSE))
}
for (txt_var in glb_txt_vars) {
re_str <- "\\b(Fort|Ft\\.|Hong|Las|Los|New|Puerto|Saint|San|St\\.)( |-)(\\w)+"
print(sprintf("Remaining #%s# terms in %s: ", re_str, txt_var))
txt_vctr <- glb_txt_lst[[txt_var]]
print(orderBy(~ -.n +pattern, subset(chk_pattern_freq(re_str, ignore.case=FALSE),
grepl("( |-)[[:upper:]]", pattern))))
print(" consider cleaning if relevant to problem domain; geography name; .n > 1")
#grep("New G", txt_vctr, value=TRUE, ignore.case=FALSE)
#grep("St\\. Wins", txt_vctr, value=TRUE, ignore.case=FALSE)
}
for (txt_var in glb_txt_vars) {
re_str <- "\\b(N|S|E|W|C)( |\\.)(\\w)+"
print(sprintf("Remaining #%s# terms in %s: ", re_str, txt_var))
txt_vctr <- glb_txt_lst[[txt_var]]
print(orderBy(~ -.n +pattern, subset(chk_pattern_freq(re_str, ignore.case=FALSE),
grepl(".", pattern))))
#grep("N Weaver", txt_vctr, value=TRUE, ignore.case=FALSE)
}
for (txt_var in glb_txt_vars) {
re_str <- "\\b(North|South|East|West|Central)( |\\.)(\\w)+"
print(sprintf("Remaining #%s# terms in %s: ", re_str, txt_var))
txt_vctr <- glb_txt_lst[[txt_var]]
print(orderBy(~ -.n +pattern, subset(chk_pattern_freq(re_str, ignore.case=FALSE),
grepl(".", pattern))))
#grep("Central (African|Bankers|Cast|Italy|Role|Spring)", txt_vctr, value=TRUE, ignore.case=FALSE)
#grep("East (Africa|Berlin|London|Poland|Rivals|Spring)", txt_vctr, value=TRUE, ignore.case=FALSE)
#grep("North (American|Korean|West)", txt_vctr, value=TRUE, ignore.case=FALSE)
#grep("South (Pacific|Street)", txt_vctr, value=TRUE, ignore.case=FALSE)
#grep("St\\. Martins", txt_vctr, value=TRUE, ignore.case=FALSE)
}
find_cmpnd_wrds <- function(txt_vctr) {
txt_corpus <- Corpus(VectorSource(txt_vctr))
txt_corpus <- tm_map(txt_corpus, tolower)
txt_corpus <- tm_map(txt_corpus, PlainTextDocument)
txt_corpus <- tm_map(txt_corpus, removePunctuation,
preserve_intra_word_dashes=TRUE)
full_Tf_DTM <- DocumentTermMatrix(txt_corpus,
control=list(weighting=weightTf))
print(" Full TermMatrix:"); print(full_Tf_DTM)
full_Tf_mtrx <- as.matrix(full_Tf_DTM)
rownames(full_Tf_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
full_Tf_vctr <- colSums(full_Tf_mtrx)
names(full_Tf_vctr) <- dimnames(full_Tf_DTM)[[2]]
#grep("year", names(full_Tf_vctr), value=TRUE)
#which.max(full_Tf_mtrx[, "yearlong"])
full_Tf_df <- as.data.frame(full_Tf_vctr)
names(full_Tf_df) <- "Tf.full"
full_Tf_df$term <- rownames(full_Tf_df)
#full_Tf_df$freq.full <- colSums(full_Tf_mtrx != 0)
full_Tf_df <- orderBy(~ -Tf.full, full_Tf_df)
cmpnd_Tf_df <- full_Tf_df[grep("-", full_Tf_df$term, value=TRUE) ,]
filter_df <- read.csv("mytxt_compound.csv", comment.char="#", strip.white=TRUE)
cmpnd_Tf_df$filter <- FALSE
for (row_ix in 1:nrow(filter_df))
cmpnd_Tf_df[!cmpnd_Tf_df$filter, "filter"] <-
grepl(filter_df[row_ix, "rex_str"],
cmpnd_Tf_df[!cmpnd_Tf_df$filter, "term"], ignore.case=TRUE)
cmpnd_Tf_df <- subset(cmpnd_Tf_df, !filter)
# Bug in tm_map(txt_corpus, removePunctuation, preserve_intra_word_dashes=TRUE) ???
# "net-a-porter" gets converted to "net-aporter"
#grep("net-a-porter", txt_vctr, ignore.case=TRUE, value=TRUE)
#grep("maser-laser", txt_vctr, ignore.case=TRUE, value=TRUE)
#txt_corpus[[which(grepl("net-a-porter", txt_vctr, ignore.case=TRUE))]]
#grep("\\b(across|longer)-(\\w)", cmpnd_Tf_df$term, ignore.case=TRUE, value=TRUE)
#grep("(\\w)-(affected|term)\\b", cmpnd_Tf_df$term, ignore.case=TRUE, value=TRUE)
print(sprintf("nrow(cmpnd_Tf_df): %d", nrow(cmpnd_Tf_df)))
myprint_df(cmpnd_Tf_df)
}
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "process.text_reporting_compound_terms"), major.inc=FALSE)
for (txt_var in glb_txt_vars) {
print(sprintf("Remaining compound terms in %s: ", txt_var))
txt_vctr <- glb_txt_lst[[txt_var]]
# find_cmpnd_wrds(txt_vctr)
#grep("thirty-five", txt_vctr, ignore.case=TRUE, value=TRUE)
#rex_str <- glb_txt_map_df[grepl("hirty", glb_txt_map_df$rex_str), "rex_str"]
}
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "build.corpus"), major.inc=TRUE)
glb_corpus_lst <- list()
print(sprintf("Building glb_corpus_lst..."))
glb_corpus_lst <- foreach(txt_var=glb_txt_vars) %dopar% {
# for (txt_var in glb_txt_vars) {
txt_corpus <- Corpus(VectorSource(glb_txt_lst[[txt_var]]))
txt_corpus <- tm_map(txt_corpus, tolower) #nuppr
txt_corpus <- tm_map(txt_corpus, PlainTextDocument)
txt_corpus <- tm_map(txt_corpus, removePunctuation) #npnct<chr_ix>
# txt-corpus <- tm_map(txt_corpus, content_transformer(function(x, pattern) gsub(pattern, "", x))
# Not to be run in production
inspect_terms <- function() {
full_Tf_DTM <- DocumentTermMatrix(txt_corpus,
control=list(weighting=weightTf))
print(" Full TermMatrix:"); print(full_Tf_DTM)
full_Tf_mtrx <- as.matrix(full_Tf_DTM)
rownames(full_Tf_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
full_Tf_vctr <- colSums(full_Tf_mtrx)
names(full_Tf_vctr) <- dimnames(full_Tf_DTM)[[2]]
#grep("year", names(full_Tf_vctr), value=TRUE)
#which.max(full_Tf_mtrx[, "yearlong"])
full_Tf_df <- as.data.frame(full_Tf_vctr)
names(full_Tf_df) <- "Tf.full"
full_Tf_df$term <- rownames(full_Tf_df)
#full_Tf_df$freq.full <- colSums(full_Tf_mtrx != 0)
full_Tf_df <- orderBy(~ -Tf.full +term, full_Tf_df)
print(myplot_histogram(full_Tf_df, "Tf.full"))
myprint_df(full_Tf_df)
#txt_corpus[[which(grepl("zun", txt_vctr, ignore.case=TRUE))]]
digit_terms_df <- subset(full_Tf_df, grepl("[[:digit:]]", term))
myprint_df(digit_terms_df)
return(full_Tf_df)
}
#print("RemovePunct:"); remove_punct_Tf_df <- inspect_terms()
txt_corpus <- tm_map(txt_corpus, removeWords,
c(glb_append_stop_words[[txt_var]],
stopwords("english"))) #nstopwrds
#print("StoppedWords:"); stopped_words_Tf_df <- inspect_terms()
txt_corpus <- tm_map(txt_corpus, stemDocument) #Features for lost information: Difference/ratio in density of full_TfIdf_DTM ???
#txt_corpus <- tm_map(txt_corpus, content_transformer(stemDocument))
#print("StemmedWords:"); stemmed_words_Tf_df <- inspect_terms()
#stemmed_stopped_Tf_df <- merge(stemmed_words_Tf_df, stopped_words_Tf_df, by="term", all=TRUE, suffixes=c(".stem", ".stop"))
#myprint_df(stemmed_stopped_Tf_df)
#print(subset(stemmed_stopped_Tf_df, grepl("compan", term)))
#glb_corpus_lst[[txt_var]] <- txt_corpus
}
names(glb_corpus_lst) <- glb_txt_vars
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "extract.DTM"), major.inc=TRUE)
glb_full_DTM_lst <- list(); glb_sprs_DTM_lst <- list();
for (txt_var in glb_txt_vars) {
print(sprintf("Extracting TfIDf terms for %s...", txt_var))
txt_corpus <- glb_corpus_lst[[txt_var]]
# full_Tf_DTM <- DocumentTermMatrix(txt_corpus,
# control=list(weighting=weightTf))
full_TfIdf_DTM <- DocumentTermMatrix(txt_corpus,
control=list(weighting=weightTfIdf))
sprs_TfIdf_DTM <- removeSparseTerms(full_TfIdf_DTM,
glb_sprs_thresholds[txt_var])
# glb_full_DTM_lst[[txt_var]] <- full_Tf_DTM
# glb_sprs_DTM_lst[[txt_var]] <- sprs_Tf_DTM
glb_full_DTM_lst[[txt_var]] <- full_TfIdf_DTM
glb_sprs_DTM_lst[[txt_var]] <- sprs_TfIdf_DTM
}
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "report.DTM"), major.inc=TRUE)
for (txt_var in glb_txt_vars) {
print(sprintf("Reporting TfIDf terms for %s...", txt_var))
full_TfIdf_DTM <- glb_full_DTM_lst[[txt_var]]
sprs_TfIdf_DTM <- glb_sprs_DTM_lst[[txt_var]]
print(" Full TermMatrix:"); print(full_TfIdf_DTM)
full_TfIdf_mtrx <- as.matrix(full_TfIdf_DTM)
rownames(full_TfIdf_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
full_TfIdf_vctr <- colSums(full_TfIdf_mtrx)
names(full_TfIdf_vctr) <- dimnames(full_TfIdf_DTM)[[2]]
#grep("scene", names(full_TfIdf_vctr), value=TRUE)
#which.max(full_TfIdf_mtrx[, "yearlong"])
full_TfIdf_df <- as.data.frame(full_TfIdf_vctr)
names(full_TfIdf_df) <- "TfIdf.full"
full_TfIdf_df$term <- rownames(full_TfIdf_df)
full_TfIdf_df$freq.full <- colSums(full_TfIdf_mtrx != 0)
full_TfIdf_df <- orderBy(~ -TfIdf.full, full_TfIdf_df)
print(" Sparse TermMatrix:"); print(sprs_TfIdf_DTM)
sprs_TfIdf_vctr <- colSums(as.matrix(sprs_TfIdf_DTM))
names(sprs_TfIdf_vctr) <- dimnames(sprs_TfIdf_DTM)[[2]]
sprs_TfIdf_df <- as.data.frame(sprs_TfIdf_vctr)
names(sprs_TfIdf_df) <- "TfIdf.sprs"
sprs_TfIdf_df$term <- rownames(sprs_TfIdf_df)
sprs_TfIdf_df$freq.sprs <- colSums(as.matrix(sprs_TfIdf_DTM) != 0)
sprs_TfIdf_df <- orderBy(~ -TfIdf.sprs, sprs_TfIdf_df)
terms_TfIdf_df <- merge(full_TfIdf_df, sprs_TfIdf_df, all.x=TRUE)
terms_TfIdf_df$in.sprs <- !is.na(terms_TfIdf_df$freq.sprs)
plt_TfIdf_df <- subset(terms_TfIdf_df,
TfIdf.full >= min(terms_TfIdf_df$TfIdf.sprs, na.rm=TRUE))
plt_TfIdf_df$label <- ""
plt_TfIdf_df[is.na(plt_TfIdf_df$TfIdf.sprs), "label"] <-
plt_TfIdf_df[is.na(plt_TfIdf_df$TfIdf.sprs), "term"]
glb_important_terms[[txt_var]] <- union(glb_important_terms[[txt_var]],
plt_TfIdf_df[is.na(plt_TfIdf_df$TfIdf.sprs), "term"])
print(myplot_scatter(plt_TfIdf_df, "freq.full", "TfIdf.full",
colorcol_name="in.sprs") +
geom_text(aes(label=label), color="Black", size=3.5))
melt_TfIdf_df <- orderBy(~ -value, melt(terms_TfIdf_df, id.var="term"))
print(ggplot(melt_TfIdf_df, aes(value, color=variable)) + stat_ecdf() +
geom_hline(yintercept=glb_sprs_thresholds[txt_var],
linetype = "dotted"))
melt_TfIdf_df <- orderBy(~ -value,
melt(subset(terms_TfIdf_df, !is.na(TfIdf.sprs)), id.var="term"))
print(myplot_hbar(melt_TfIdf_df, "term", "value",
colorcol_name="variable"))
melt_TfIdf_df <- orderBy(~ -value,
melt(subset(terms_TfIdf_df, is.na(TfIdf.sprs)), id.var="term"))
print(myplot_hbar(head(melt_TfIdf_df, 10), "term", "value",
colorcol_name="variable"))
}
# sav_full_DTM_lst <- glb_full_DTM_lst
# sav_sprs_DTM_lst <- glb_sprs_DTM_lst
# print(identical(sav_glb_corpus_lst, glb_corpus_lst))
# print(all.equal(length(sav_glb_corpus_lst), length(glb_corpus_lst)))
# print(all.equal(names(sav_glb_corpus_lst), names(glb_corpus_lst)))
# print(all.equal(sav_glb_corpus_lst[["Headline"]], glb_corpus_lst[["Headline"]]))
# print(identical(sav_full_DTM_lst, glb_full_DTM_lst))
# print(identical(sav_sprs_DTM_lst, glb_sprs_DTM_lst))
rm(full_TfIdf_mtrx, full_TfIdf_df, melt_TfIdf_df, terms_TfIdf_df)
# Create txt features
if ((length(glb_txt_vars) > 1) &&
(length(unique(pfxs <- sapply(glb_txt_vars,
function(txt) toupper(substr(txt, 1, 1))))) < length(glb_txt_vars)))
stop("Prefixes for corpus freq terms not unique: ", pfxs)
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "bind.DTM"),
major.inc=TRUE)
for (txt_var in glb_txt_vars) {
print(sprintf("Binding DTM for %s...", txt_var))
txt_var_pfx <- toupper(substr(txt_var, 1, 1))
txt_X_df <- as.data.frame(as.matrix(glb_sprs_DTM_lst[[txt_var]]))
colnames(txt_X_df) <- paste(txt_var_pfx, ".T.",
make.names(colnames(txt_X_df)), sep="")
rownames(txt_X_df) <- rownames(glb_allobs_df) # warning otherwise
# plt_X_df <- cbind(txt_X_df, glb_allobs_df[, c(glb_id_var, glb_rsp_var)])
# print(myplot_box(df=plt_X_df, ycol_names="H.T.today", xcol_name=glb_rsp_var))
# log_X_df <- log(1 + txt_X_df)
# colnames(log_X_df) <- paste(colnames(txt_X_df), ".log", sep="")
# plt_X_df <- cbind(log_X_df, glb_allobs_df[, c(glb_id_var, glb_rsp_var)])
# print(myplot_box(df=plt_X_df, ycol_names="H.T.today.log", xcol_name=glb_rsp_var))
glb_allobs_df <- cbind(glb_allobs_df, txt_X_df) # TfIdf is normalized
#glb_allobs_df <- cbind(glb_allobs_df, log_X_df) # if using non-normalized metrics
}
#identical(chk_entity_df, glb_allobs_df)
#chk_entity_df <- glb_allobs_df
extract.features_chunk_df <- myadd_chunk(extract.features_chunk_df,
paste0("extract.features_", "bind.DXM"),
major.inc=TRUE)
#sav_allobs_df <- glb_allobs_df
glb_punct_vctr <- c("!", "\"", "#", "\\$", "%", "&", "'",
"\\(|\\)",# "\\(", "\\)",
"\\*", "\\+", ",", "-", "\\.", "/", ":", ";",
"<|>", # "<",
"=",
# ">",
"\\?", "@", "\\[", "\\\\", "\\]", "^", "_", "`",
"\\{", "\\|", "\\}", "~")
txt_X_df <- glb_allobs_df[, c(glb_id_var, ".rnorm"), FALSE]
txt_X_df <- foreach(txt_var=glb_txt_vars, .combine=cbind) %dopar% {
#for (txt_var in glb_txt_vars) {
print(sprintf("Binding DXM for %s...", txt_var))
txt_var_pfx <- toupper(substr(txt_var, 1, 1))
#txt_X_df <- glb_allobs_df[, c(glb_id_var, ".rnorm"), FALSE]
txt_full_DTM_mtrx <- as.matrix(glb_full_DTM_lst[[txt_var]])
rownames(txt_full_DTM_mtrx) <- rownames(glb_allobs_df) # print undreadable otherwise
#print(txt_full_DTM_mtrx[txt_full_DTM_mtrx[, "ebola"] != 0, "ebola"])
# Create <txt_var>.T.<term> for glb_important_terms
for (term in glb_important_terms[[txt_var]])
txt_X_df[, paste0(txt_var_pfx, ".T.", make.names(term))] <-
txt_full_DTM_mtrx[, term]
# Create <txt_var>.nwrds.log & .nwrds.unq.log
txt_X_df[, paste0(txt_var_pfx, ".nwrds.log")] <-
log(1 + mycount_pattern_occ("\\w+", glb_txt_lst[[txt_var]]))
txt_X_df[, paste0(txt_var_pfx, ".nwrds.unq.log")] <-
log(1 + rowSums(txt_full_DTM_mtrx != 0))
txt_X_df[, paste0(txt_var_pfx, ".sum.TfIdf")] <-
rowSums(txt_full_DTM_mtrx)
txt_X_df[, paste0(txt_var_pfx, ".ratio.sum.TfIdf.nwrds")] <-
txt_X_df[, paste0(txt_var_pfx, ".sum.TfIdf")] /
(exp(txt_X_df[, paste0(txt_var_pfx, ".nwrds.log")]) - 1)
txt_X_df[is.nan(txt_X_df[, paste0(txt_var_pfx, ".ratio.sum.TfIdf.nwrds")]),
paste0(txt_var_pfx, ".ratio.sum.TfIdf.nwrds")] <- 0
# Create <txt_var>.nchrs.log
txt_X_df[, paste0(txt_var_pfx, ".nchrs.log")] <-
log(1 + mycount_pattern_occ(".", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".nuppr.log")] <-
log(1 + mycount_pattern_occ("[[:upper:]]", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".ndgts.log")] <-
log(1 + mycount_pattern_occ("[[:digit:]]", glb_allobs_df[, txt_var]))
# Create <txt_var>.npnct?.log
# would this be faster if it's iterated over each row instead of
# each created column ???
for (punct_ix in 1:length(glb_punct_vctr)) {
# smp0 <- " "
# smp1 <- "! \" # $ % & ' ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ ` { | } ~"
# smp2 <- paste(smp1, smp1, sep=" ")
# print(sprintf("Testing %s pattern:", glb_punct_vctr[punct_ix]))
# results <- mycount_pattern_occ(glb_punct_vctr[punct_ix], c(smp0, smp1, smp2))
# names(results) <- NULL; print(results)
txt_X_df[,
paste0(txt_var_pfx, ".npnct", sprintf("%02d", punct_ix), ".log")] <-
log(1 + mycount_pattern_occ(glb_punct_vctr[punct_ix],
glb_allobs_df[, txt_var]))
}
# print(head(glb_allobs_df[glb_allobs_df[, "A.npnct23.log"] > 0,
# c("UniqueID", "Popular", "Abstract", "A.npnct23.log")]))
# Create <txt_var>.nstopwrds.log & <txt_var>ratio.nstopwrds.nwrds
stop_words_rex_str <- paste0("\\b(", paste0(c(glb_append_stop_words[[txt_var]],
stopwords("english")), collapse="|"),
")\\b")
txt_X_df[, paste0(txt_var_pfx, ".nstopwrds", ".log")] <-
log(1 + mycount_pattern_occ(stop_words_rex_str, glb_txt_lst[[txt_var]]))
txt_X_df[, paste0(txt_var_pfx, ".ratio.nstopwrds.nwrds")] <-
exp(txt_X_df[, paste0(txt_var_pfx, ".nstopwrds", ".log")] -
txt_X_df[, paste0(txt_var_pfx, ".nwrds", ".log")])
# Create <txt_var>.P.http
txt_X_df[, paste(txt_var_pfx, ".P.http", sep="")] <-
as.integer(0 + mycount_pattern_occ("http", glb_allobs_df[, txt_var]))
# Create user-specified pattern vectors
# <txt_var>.P.year.colon
txt_X_df[, paste0(txt_var_pfx, ".P.year.colon")] <-
as.integer(0 + mycount_pattern_occ("[0-9]{4}:", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.daily.clip.report")] <-
as.integer(0 + mycount_pattern_occ("Daily Clip Report", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.fashion.week")] <-
as.integer(0 + mycount_pattern_occ("Fashion Week", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.first.draft")] <-
as.integer(0 + mycount_pattern_occ("First Draft", glb_allobs_df[, txt_var]))
#sum(mycount_pattern_occ("Metropolitan Diary:", glb_allobs_df$Abstract) > 0)
if (txt_var %in% c("Snippet", "Abstract")) {
txt_X_df[, paste0(txt_var_pfx, ".P.metropolitan.diary.colon")] <-
as.integer(0 + mycount_pattern_occ("Metropolitan Diary:",
glb_allobs_df[, txt_var]))
}
#sum(mycount_pattern_occ("[0-9]{4}:", glb_allobs_df$Headline) > 0)
#sum(mycount_pattern_occ("Quandary(.*)(?=:)", glb_allobs_df$Headline, perl=TRUE) > 0)
#sum(mycount_pattern_occ("No Comment(.*):", glb_allobs_df$Headline) > 0)
#sum(mycount_pattern_occ("Friday Night Music:", glb_allobs_df$Headline) > 0)
if (txt_var %in% c("Headline")) {
txt_X_df[, paste0(txt_var_pfx, ".P.facts.figures")] <-
as.integer(0 + mycount_pattern_occ("Facts & Figures:", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.friday.night.music")] <-
as.integer(0 + mycount_pattern_occ("Friday Night Music", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.no.comment.colon")] <-
as.integer(0 + mycount_pattern_occ("No Comment(.*):", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.on.this.day")] <-
as.integer(0 + mycount_pattern_occ("On This Day", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.quandary")] <-
as.integer(0 + mycount_pattern_occ("Quandary(.*)(?=:)", glb_allobs_df[, txt_var], perl=TRUE))
txt_X_df[, paste0(txt_var_pfx, ".P.readers.respond")] <-
as.integer(0 + mycount_pattern_occ("Readers Respond", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.recap.colon")] <-
as.integer(0 + mycount_pattern_occ("Recap:", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.s.notebook")] <-
as.integer(0 + mycount_pattern_occ("s Notebook", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.today.in.politic")] <-
as.integer(0 + mycount_pattern_occ("Today in Politic", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.today.in.smallbusiness")] <-
as.integer(0 + mycount_pattern_occ("Today in Small Business:", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.verbatim.colon")] <-
as.integer(0 + mycount_pattern_occ("Verbatim:", glb_allobs_df[, txt_var]))
txt_X_df[, paste0(txt_var_pfx, ".P.what.we.are")] <-
as.integer(0 + mycount_pattern_occ("What We're", glb_allobs_df[, txt_var]))
}
#summary(glb_allobs_df[ ,grep("P.on.this.day", names(glb_allobs_df), value=TRUE)])
txt_X_df <- subset(txt_X_df, select=-.rnorm)
txt_X_df <- txt_X_df[, -grep(glb_id_var, names(txt_X_df), fixed=TRUE), FALSE]
#glb_allobs_df <- cbind(glb_allobs_df, txt_X_df)
}
glb_allobs_df <- cbind(glb_allobs_df, txt_X_df)
#myplot_box(glb_allobs_df, "A.sum.TfIdf", glb_rsp_var)
# Generate summaries
# print(summary(glb_allobs_df))
# print(sapply(names(glb_allobs_df), function(col) sum(is.na(glb_allobs_df[, col]))))
# print(summary(glb_trnobs_df))
# print(sapply(names(glb_trnobs_df), function(col) sum(is.na(glb_trnobs_df[, col]))))
# print(summary(glb_newobs_df))
# print(sapply(names(glb_newobs_df), function(col) sum(is.na(glb_newobs_df[, col]))))
glb_exclude_vars_as_features <- union(glb_exclude_vars_as_features,
glb_txt_vars)
rm(log_X_df, txt_X_df)
}
# print(sapply(names(glb_trnobs_df), function(col) sum(is.na(glb_trnobs_df[, col]))))
# print(sapply(names(glb_newobs_df), function(col) sum(is.na(glb_newobs_df[, col]))))
# print(myplot_scatter(glb_trnobs_df, "<col1_name>", "<col2_name>", smooth=TRUE))
rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
glb_full_DTM_lst, glb_sprs_DTM_lst, txt_corpus, txt_vctr)## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'corpus_lst' not found## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'full_TfIdf_DTM' not found## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'full_TfIdf_vctr' not found## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'glb_full_DTM_lst' not found## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'glb_sprs_DTM_lst' not found## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'txt_corpus' not found## Warning in rm(corpus_lst, full_TfIdf_DTM, full_TfIdf_vctr,
## glb_full_DTM_lst, : object 'txt_vctr' not foundextract.features_chunk_df <- myadd_chunk(extract.features_chunk_df, "extract.features_end",
major.inc=TRUE)## label step_major step_minor bgn end
## 2 extract.features_factorize.str.vars 2 0 17.653 17.676
## 3 extract.features_end 3 0 17.677 NA
## elapsed
## 2 0.024
## 3 NAmyplt_chunk(extract.features_chunk_df)## label step_major step_minor bgn end
## 2 extract.features_factorize.str.vars 2 0 17.653 17.676
## 1 extract.features_bgn 1 0 17.645 17.653
## elapsed duration
## 2 0.024 0.023
## 1 0.008 0.008
## [1] "Total Elapsed Time: 17.676 secs"
# if (glb_save_envir)
# save(glb_feats_df,
# glb_allobs_df, #glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
# file=paste0(glb_out_pfx, "extract_features_dsk.RData"))
# load(paste0(glb_out_pfx, "extract_features_dsk.RData"))
replay.petrisim(pn=glb_analytics_pn,
replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs,
"data.training.all","data.new")), flip_coord=TRUE)## time trans "bgn " "fit.data.training.all " "predict.data.new " "end "
## 0.0000 multiple enabled transitions: data.training.all data.new model.selected firing: data.training.all
## 1.0000 1 2 1 0 0
## 1.0000 multiple enabled transitions: data.training.all data.new model.selected model.final data.training.all.prediction firing: data.new
## 2.0000 2 1 1 1 0
glb_chunks_df <- myadd_chunk(glb_chunks_df, "cluster.data", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 6 extract.features 3 0 17.639 18.98 1.342
## 7 cluster.data 4 0 18.981 NA NAStep 4.0: cluster data
if (glb_cluster) {
require(proxy)
#require(hash)
require(dynamicTreeCut)
# glb_hash <- hash(key=unique(glb_allobs_df$myCategory),
# values=1:length(unique(glb_allobs_df$myCategory)))
# glb_hash_lst <- hash(key=unique(glb_allobs_df$myCategory),
# values=1:length(unique(glb_allobs_df$myCategory)))
#stophere; sav_allobs_df <- glb_allobs_df;
print("Clustering features: ")
print(cluster_vars <- grep("[HSA]\\.[PT]\\.", names(glb_allobs_df), value=TRUE))
#print(cluster_vars <- grep("[HSA]\\.", names(glb_allobs_df), value=TRUE))
glb_allobs_df$.clusterid <- 1
#print(max(table(glb_allobs_df$myCategory.fctr) / 20))
for (myCategory in c("##", "Business#Business Day#Dealbook", "OpEd#Opinion#",
"Styles#U.S.#", "Business#Technology#", "Science#Health#",
"Culture#Arts#")) {
ctgry_allobs_df <- glb_allobs_df[glb_allobs_df$myCategory == myCategory, ]
dstns_dist <- dist(ctgry_allobs_df[, cluster_vars], method = "cosine")
dstns_mtrx <- as.matrix(dstns_dist)
print(sprintf("max distance(%0.4f) pair:", max(dstns_mtrx)))
row_ix <- ceiling(which.max(dstns_mtrx) / ncol(dstns_mtrx))
col_ix <- which.max(dstns_mtrx[row_ix, ])
print(ctgry_allobs_df[c(row_ix, col_ix),
c("UniqueID", "Popular", "myCategory", "Headline", cluster_vars)])
min_dstns_mtrx <- dstns_mtrx
diag(min_dstns_mtrx) <- 1
print(sprintf("min distance(%0.4f) pair:", min(min_dstns_mtrx)))
row_ix <- ceiling(which.min(min_dstns_mtrx) / ncol(min_dstns_mtrx))
col_ix <- which.min(min_dstns_mtrx[row_ix, ])
print(ctgry_allobs_df[c(row_ix, col_ix),
c("UniqueID", "Popular", "myCategory", "Headline", cluster_vars)])
clusters <- hclust(dstns_dist, method = "ward.D2")
#plot(clusters, labels=NULL, hang=-1)
myplclust(clusters, lab.col=unclass(ctgry_allobs_df[, glb_rsp_var]))
#clusterGroups = cutree(clusters, k=7)
clusterGroups <- cutreeDynamic(clusters, minClusterSize=20, method="tree", deepSplit=0)
# Unassigned groups are labeled 0; the largest group has label 1
table(clusterGroups, ctgry_allobs_df[, glb_rsp_var], useNA="ifany")
#print(ctgry_allobs_df[which(clusterGroups == 1), c("UniqueID", "Popular", "Headline")])
#print(ctgry_allobs_df[(clusterGroups == 1) & !is.na(ctgry_allobs_df$Popular) & (ctgry_allobs_df$Popular==1), c("UniqueID", "Popular", "Headline")])
clusterGroups[clusterGroups == 0] <- 1
table(clusterGroups, ctgry_allobs_df[, glb_rsp_var], useNA="ifany")
#summary(factor(clusterGroups))
# clusterGroups <- clusterGroups +
# 100 * # has to be > max(table(glb_allobs_df$myCategory.fctr) / minClusterSize=20)
# which(levels(glb_allobs_df$myCategory.fctr) == myCategory)
# table(clusterGroups, ctgry_allobs_df[, glb_rsp_var], useNA="ifany")
# add to glb_allobs_df - then split the data again
glb_allobs_df[glb_allobs_df$myCategory==myCategory,]$.clusterid <- clusterGroups
#print(unique(glb_allobs_df$.clusterid))
#print(glb_feats_df[glb_feats_df$id == ".clusterid.fctr", ])
}
ctgry_xtab_df <- orderBy(reformulate(c("-", ".n")),
mycreate_sqlxtab_df(glb_allobs_df,
c("myCategory", ".clusterid", glb_rsp_var)))
ctgry_cast_df <- orderBy(~ -Y -NA, dcast(ctgry_xtab_df,
myCategory + .clusterid ~
Popular.fctr, sum, value.var=".n"))
print(ctgry_cast_df)
#print(orderBy(~ myCategory -Y -NA, ctgry_cast_df))
# write.table(ctgry_cast_df, paste0(glb_out_pfx, "ctgry_clst.csv"),
# row.names=FALSE)
print(ctgry_sum_tbl <- table(glb_allobs_df$myCategory, glb_allobs_df$.clusterid,
glb_allobs_df[, glb_rsp_var],
useNA="ifany"))
# dsp_obs(.clusterid=1, myCategory="OpEd#Opinion#",
# cols=c("UniqueID", "Popular", "myCategory", ".clusterid", "Headline"),
# all=TRUE)
glb_allobs_df$.clusterid.fctr <- as.factor(glb_allobs_df$.clusterid)
glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features,
".clusterid")
glb_interaction_only_features["myCategory.fctr"] <- c(".clusterid.fctr")
glb_exclude_vars_as_features <- c(glb_exclude_vars_as_features,
cluster_vars)
}
# Re-partition
glb_trnobs_df <- subset(glb_allobs_df, .src == "Train")
glb_newobs_df <- subset(glb_allobs_df, .src == "Test")
glb_chunks_df <- myadd_chunk(glb_chunks_df, "select.features", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 7 cluster.data 4 0 18.981 19.252 0.271
## 8 select.features 5 0 19.253 NA NAStep 5.0: select features
print(glb_feats_df <- myselect_features(entity_df=glb_trnobs_df,
exclude_vars_as_features=glb_exclude_vars_as_features,
rsp_var=glb_rsp_var))## id
## Worry.About.Info Worry.About.Info
## Privacy.Laws.Effective Privacy.Laws.Effective
## Worry.About.Info.my.fctr Worry.About.Info.my.fctr
## Privacy.Laws.Effective.my.fctr Privacy.Laws.Effective.my.fctr
## Tried.Masking.Identity Tried.Masking.Identity
## Anonymity.Possible Anonymity.Possible
## Age.my.fctr Age.my.fctr
## Tried.Masking.Identity.my.fctr Tried.Masking.Identity.my.fctr
## Internet.Use Internet.Use
## Internet.Use.my Internet.Use.my
## Anonymity.Possible.my.fctr Anonymity.Possible.my.fctr
## Age Age
## Sex.fctr Sex.fctr
## Conservativeness Conservativeness
## Conservativeness.my.fctr Conservativeness.my.fctr
## Region.fctr Region.fctr
## State.fctr State.fctr
## Smartphone Smartphone
## Info.On.Internet.my.fctr Info.On.Internet.my.fctr
## Info.On.Internet Info.On.Internet
## .rnorm .rnorm
## Smartphone.my.fctr Smartphone.my.fctr
## cor.y exclude.as.feat cor.y.abs
## Worry.About.Info 0.2731098859 1 0.2731098859
## Privacy.Laws.Effective -0.2646162683 1 0.2646162683
## Worry.About.Info.my.fctr 0.2590726457 0 0.2590726457
## Privacy.Laws.Effective.my.fctr -0.2089672738 0 0.2089672738
## Tried.Masking.Identity 0.0917151958 1 0.0917151958
## Anonymity.Possible -0.0900636172 1 0.0900636172
## Age.my.fctr 0.0784486053 0 0.0784486053
## Tried.Masking.Identity.my.fctr 0.0738452219 0 0.0738452219
## Internet.Use 0.0716537180 1 0.0716537180
## Internet.Use.my 0.0716537180 0 0.0716537180
## Anonymity.Possible.my.fctr -0.0705772584 0 0.0705772584
## Age 0.0586258396 1 0.0586258396
## Sex.fctr 0.0568208798 0 0.0568208798
## Conservativeness 0.0475530736 1 0.0475530736
## Conservativeness.my.fctr 0.0380593579 0 0.0380593579
## Region.fctr -0.0373439487 0 0.0373439487
## State.fctr -0.0326536598 1 0.0326536598
## Smartphone 0.0112852450 1 0.0112852450
## Info.On.Internet.my.fctr -0.0052073661 0 0.0052073661
## Info.On.Internet 0.0045589909 1 0.0045589909
## .rnorm -0.0036694388 0 0.0036694388
## Smartphone.my.fctr -0.0007627864 0 0.0007627864# sav_feats_df <- glb_feats_df; glb_feats_df <- sav_feats_df
print(glb_feats_df <- orderBy(~-cor.y,
myfind_cor_features(feats_df=glb_feats_df, obs_df=glb_trnobs_df,
rsp_var=glb_rsp_var)))## Loading required package: reshape2## id cor.y exclude.as.feat
## 21 Worry.About.Info 0.2731098859 1
## 22 Worry.About.Info.my.fctr 0.2590726457 0
## 19 Tried.Masking.Identity 0.0917151958 1
## 3 Age.my.fctr 0.0784486053 0
## 20 Tried.Masking.Identity.my.fctr 0.0738452219 0
## 10 Internet.Use 0.0716537180 1
## 11 Internet.Use.my 0.0716537180 0
## 2 Age 0.0586258396 1
## 15 Sex.fctr 0.0568208798 0
## 6 Conservativeness 0.0475530736 1
## 7 Conservativeness.my.fctr 0.0380593579 0
## 16 Smartphone 0.0112852450 1
## 8 Info.On.Internet 0.0045589909 1
## 17 Smartphone.my.fctr -0.0007627864 0
## 1 .rnorm -0.0036694388 0
## 9 Info.On.Internet.my.fctr -0.0052073661 0
## 18 State.fctr -0.0326536598 1
## 14 Region.fctr -0.0373439487 0
## 5 Anonymity.Possible.my.fctr -0.0705772584 0
## 4 Anonymity.Possible -0.0900636172 1
## 13 Privacy.Laws.Effective.my.fctr -0.2089672738 0
## 12 Privacy.Laws.Effective -0.2646162683 1
## cor.y.abs cor.high.X freqRatio percentUnique zeroVar nzv myNearZV
## 21 0.2731098859 NA 1.102273 0.3597122 FALSE FALSE FALSE
## 22 0.2590726457 NA 1.102273 0.5395683 FALSE FALSE FALSE
## 19 0.0917151958 NA 5.122222 0.3597122 FALSE FALSE FALSE
## 3 0.0784486053 NA 1.239726 1.0791367 FALSE FALSE FALSE
## 20 0.0738452219 NA 5.122222 0.5395683 FALSE FALSE FALSE
## 10 0.0716537180 NA 54.600000 0.3597122 FALSE TRUE FALSE
## 11 0.0716537180 NA 54.600000 0.3597122 FALSE TRUE FALSE
## 2 0.0586258396 NA 1.055556 12.2302158 FALSE FALSE FALSE
## 15 0.0568208798 NA 1.114068 0.3597122 FALSE FALSE FALSE
## 6 0.0475530736 NA 1.069364 0.8992806 FALSE FALSE FALSE
## 7 0.0380593579 NA 1.069364 1.0791367 FALSE FALSE FALSE
## 16 0.0112852450 NA 1.737374 0.3597122 FALSE FALSE FALSE
## 8 0.0045589909 NA 1.027397 2.1582734 FALSE FALSE FALSE
## 17 0.0007627864 NA 1.737374 0.5395683 FALSE FALSE FALSE
## 1 0.0036694388 NA 1.000000 100.0000000 FALSE FALSE FALSE
## 9 0.0052073661 NA 1.027397 2.1582734 FALSE FALSE FALSE
## 18 0.0326536598 NA 1.441860 8.6330935 FALSE FALSE FALSE
## 14 0.0373439487 NA 1.369128 0.7194245 FALSE FALSE FALSE
## 5 0.0705772584 NA 1.671717 0.5395683 FALSE FALSE FALSE
## 4 0.0900636172 NA 1.671717 0.3597122 FALSE FALSE FALSE
## 13 0.2089672738 NA 2.762963 0.5395683 FALSE FALSE FALSE
## 12 0.2646162683 NA 2.762963 0.3597122 FALSE FALSE FALSE
## is.cor.y.abs.low
## 21 FALSE
## 22 FALSE
## 19 FALSE
## 3 FALSE
## 20 FALSE
## 10 FALSE
## 11 FALSE
## 2 FALSE
## 15 FALSE
## 6 FALSE
## 7 FALSE
## 16 FALSE
## 8 FALSE
## 17 TRUE
## 1 FALSE
## 9 FALSE
## 18 FALSE
## 14 FALSE
## 5 FALSE
## 4 FALSE
## 13 FALSE
## 12 FALSE#subset(glb_feats_df, id %in% c("A.nuppr.log", "S.nuppr.log"))
print(myplot_scatter(glb_feats_df, "percentUnique", "freqRatio",
colorcol_name="myNearZV", jitter=TRUE) +
geom_point(aes(shape=nzv)) + xlim(-5, 25))## Warning in myplot_scatter(glb_feats_df, "percentUnique", "freqRatio",
## colorcol_name = "myNearZV", : converting myNearZV to class:factor## Warning in loop_apply(n, do.ply): Removed 1 rows containing missing values
## (geom_point).## Warning in loop_apply(n, do.ply): Removed 1 rows containing missing values
## (geom_point).## Warning in loop_apply(n, do.ply): Removed 1 rows containing missing values
## (geom_point).
print(subset(glb_feats_df, myNearZV))## [1] id cor.y exclude.as.feat cor.y.abs
## [5] cor.high.X freqRatio percentUnique zeroVar
## [9] nzv myNearZV is.cor.y.abs.low
## <0 rows> (or 0-length row.names)glb_allobs_df <- glb_allobs_df[, setdiff(names(glb_allobs_df),
subset(glb_feats_df, myNearZV)$id)]
if (!is.null(glb_interaction_only_features))
glb_feats_df[glb_feats_df$id %in% glb_interaction_only_features, "interaction.feat"] <-
names(glb_interaction_only_features) else
glb_feats_df$interaction.feat <- NA
mycheck_problem_data(glb_allobs_df, terminate = TRUE)## [1] "numeric data missing in : "
## Internet.Use Smartphone Age
## 1 43 27
## Conservativeness Info.On.Internet Worry.About.Info
## 62 210 212
## Privacy.Importance Anonymity.Possible Tried.Masking.Identity
## 215 249 218
## Privacy.Laws.Effective
## 108
## [1] "numeric data w/ 0s in : "
## Internet.Use Smartphone
## 226 472
## Info.On.Internet Worry.About.Info
## 105 404
## Privacy.Importance Anonymity.Possible
## 43 475
## Tried.Masking.Identity Privacy.Laws.Effective
## 656 660
## Internet.Use.my Anonymity.Possible.my.fctr
## 227 475
## Info.On.Internet.my.fctr Privacy.Laws.Effective.my.fctr
## 105 660
## Smartphone.my.fctr Tried.Masking.Identity.my.fctr
## 472 656
## Worry.About.Info.my.fctr
## 404
## [1] "numeric data w/ Infs in : "
## named integer(0)
## [1] "numeric data w/ NaNs in : "
## named integer(0)
## [1] "string data missing in : "
## Sex State Region .rownames
## 0 0 0 0# glb_allobs_df %>% filter(is.na(Married.fctr)) %>% tbl_df()
# glb_allobs_df %>% count(Married.fctr)
# levels(glb_allobs_df$Married.fctr)
glb_chunks_df <- myadd_chunk(glb_chunks_df, "partition.data.training", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 8 select.features 5 0 19.253 19.878 0.626
## 9 partition.data.training 6 0 19.879 NA NAStep 6.0: partition data training
if (all(is.na(glb_newobs_df[, glb_rsp_var]))) {
require(caTools)
set.seed(glb_split_sample.seed)
split <- sample.split(glb_trnobs_df[, glb_rsp_var_raw],
SplitRatio=1 - (nrow(glb_newobs_df) * 1.1 / nrow(glb_trnobs_df)))
glb_fitobs_df <- glb_trnobs_df[split, ]
glb_OOBobs_df <- glb_trnobs_df[!split ,]
} else {
print(sprintf("Newdata contains non-NA data for %s; setting OOB to Newdata",
glb_rsp_var))
glb_fitobs_df <- glb_trnobs_df; glb_OOBobs_df <- glb_newobs_df
}## [1] "Newdata contains non-NA data for Privacy.Importance; setting OOB to Newdata"if (!is.null(glb_max_fitent_obs) && (nrow(glb_fitobs_df) > glb_max_fitent_obs)) {
warning("glb_fitobs_df restricted to glb_max_fitent_obs: ",
format(glb_max_fitent_obs, big.mark=","))
org_fitent_df <- glb_fitobs_df
glb_fitobs_df <-
org_fitent_df[split <- sample.split(org_fitent_df[, glb_rsp_var_raw],
SplitRatio=glb_max_fitent_obs), ]
org_fitent_df <- NULL
}
glb_allobs_df$.lcn <- ""
glb_allobs_df[glb_allobs_df[, glb_id_var] %in%
glb_fitobs_df[, glb_id_var], ".lcn"] <- "Fit"
glb_allobs_df[glb_allobs_df[, glb_id_var] %in%
glb_OOBobs_df[, glb_id_var], ".lcn"] <- "OOB"
dsp_class_dstrb <- function(obs_df, location_var, partition_var) {
xtab_df <- mycreate_xtab_df(obs_df, c(location_var, partition_var))
rownames(xtab_df) <- xtab_df[, location_var]
xtab_df <- xtab_df[, -grepl(location_var, names(xtab_df))]
print(xtab_df)
print(xtab_df / rowSums(xtab_df, na.rm=TRUE))
}
# Ensure proper splits by glb_rsp_var_raw & user-specified feature for OOB vs. new
if (!is.null(glb_category_vars)) {
if (glb_is_classification)
dsp_class_dstrb(glb_allobs_df, ".lcn", glb_rsp_var_raw)
newent_ctgry_df <- mycreate_sqlxtab_df(subset(glb_allobs_df, .src == "Test"),
glb_category_vars)
OOBobs_ctgry_df <- mycreate_sqlxtab_df(subset(glb_allobs_df, .lcn == "OOB"),
glb_category_vars)
glb_ctgry_df <- merge(newent_ctgry_df, OOBobs_ctgry_df, by=glb_category_vars
, all=TRUE, suffixes=c(".Tst", ".OOB"))
glb_ctgry_df$.freqRatio.Tst <- glb_ctgry_df$.n.Tst / sum(glb_ctgry_df$.n.Tst, na.rm=TRUE)
glb_ctgry_df$.freqRatio.OOB <- glb_ctgry_df$.n.OOB / sum(glb_ctgry_df$.n.OOB, na.rm=TRUE)
print(orderBy(~-.freqRatio.Tst-.freqRatio.OOB, glb_ctgry_df))
}
# Run this line by line
print("glb_feats_df:"); print(dim(glb_feats_df))## [1] "glb_feats_df:"## [1] 22 12sav_feats_df <- glb_feats_df
glb_feats_df <- sav_feats_df
glb_feats_df[, "rsp_var_raw"] <- FALSE
glb_feats_df[glb_feats_df$id == glb_rsp_var_raw, "rsp_var_raw"] <- TRUE
glb_feats_df$exclude.as.feat <- (glb_feats_df$exclude.as.feat == 1)
if (!is.null(glb_id_var) && glb_id_var != ".rownames")
glb_feats_df[glb_feats_df$id %in% glb_id_var, "id_var"] <- TRUE
add_feats_df <- data.frame(id=glb_rsp_var, exclude.as.feat=TRUE, rsp_var=TRUE)
row.names(add_feats_df) <- add_feats_df$id; print(add_feats_df)## id exclude.as.feat rsp_var
## Privacy.Importance Privacy.Importance TRUE TRUEglb_feats_df <- myrbind_df(glb_feats_df, add_feats_df)
if (glb_id_var != ".rownames")
print(subset(glb_feats_df, rsp_var_raw | rsp_var | id_var)) else
print(subset(glb_feats_df, rsp_var_raw | rsp_var)) ## id cor.y exclude.as.feat cor.y.abs
## Privacy.Importance Privacy.Importance NA TRUE NA
## cor.high.X freqRatio percentUnique zeroVar nzv myNearZV
## Privacy.Importance NA NA NA NA NA NA
## is.cor.y.abs.low interaction.feat rsp_var_raw rsp_var
## Privacy.Importance NA NA NA TRUEprint("glb_feats_df vs. glb_allobs_df: "); ## [1] "glb_feats_df vs. glb_allobs_df: "print(setdiff(glb_feats_df$id, names(glb_allobs_df)))## character(0)print("glb_allobs_df vs. glb_feats_df: "); ## [1] "glb_allobs_df vs. glb_feats_df: "# Ensure these are only chr vars
print(setdiff(setdiff(names(glb_allobs_df), glb_feats_df$id),
myfind_chr_cols_df(glb_allobs_df)))## character(0)#print(setdiff(setdiff(names(glb_allobs_df), glb_exclude_vars_as_features),
# glb_feats_df$id))
print("glb_allobs_df: "); print(dim(glb_allobs_df))## [1] "glb_allobs_df: "## [1] 1002 29print("glb_trnobs_df: "); print(dim(glb_trnobs_df))## [1] "glb_trnobs_df: "## [1] 556 28print("glb_fitobs_df: "); print(dim(glb_fitobs_df))## [1] "glb_fitobs_df: "## [1] 556 28print("glb_OOBobs_df: "); print(dim(glb_OOBobs_df))## [1] "glb_OOBobs_df: "## [1] 446 28print("glb_newobs_df: "); print(dim(glb_newobs_df))## [1] "glb_newobs_df: "## [1] 446 28# # Does not handle NULL or length(glb_id_var) > 1
# glb_allobs_df$.src.trn <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_trnobs_df[, glb_id_var],
# ".src.trn"] <- 1
# glb_allobs_df$.src.fit <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_fitobs_df[, glb_id_var],
# ".src.fit"] <- 1
# glb_allobs_df$.src.OOB <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_OOBobs_df[, glb_id_var],
# ".src.OOB"] <- 1
# glb_allobs_df$.src.new <- 0
# glb_allobs_df[glb_allobs_df[, glb_id_var] %in% glb_newobs_df[, glb_id_var],
# ".src.new"] <- 1
# #print(unique(glb_allobs_df[, ".src.trn"]))
# write_cols <- c(glb_feats_df$id,
# ".src.trn", ".src.fit", ".src.OOB", ".src.new")
# glb_allobs_df <- glb_allobs_df[, write_cols]
#
# tmp_feats_df <- glb_feats_df
# tmp_entity_df <- glb_allobs_df
if (glb_save_envir)
save(glb_feats_df,
glb_allobs_df, #glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
file=paste0(glb_out_pfx, "blddfs_dsk.RData"))
# load(paste0(glb_out_pfx, "blddfs_dsk.RData"))
# if (!all.equal(tmp_feats_df, glb_feats_df))
# stop("glb_feats_df r/w not working")
# if (!all.equal(tmp_entity_df, glb_allobs_df))
# stop("glb_allobs_df r/w not working")
rm(split)
glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 9 partition.data.training 6 0 19.879 20.175 0.296
## 10 fit.models 7 0 20.175 NA NAStep 7.0: fit models
# load(paste0(glb_out_pfx, "dsk.RData"))
# keep_cols <- setdiff(names(glb_allobs_df),
# grep("^.src", names(glb_allobs_df), value=TRUE))
# glb_trnobs_df <- glb_allobs_df[glb_allobs_df$.src.trn == 1, keep_cols]
# glb_fitobs_df <- glb_allobs_df[glb_allobs_df$.src.fit == 1, keep_cols]
# glb_OOBobs_df <- glb_allobs_df[glb_allobs_df$.src.OOB == 1, keep_cols]
# glb_newobs_df <- glb_allobs_df[glb_allobs_df$.src.new == 1, keep_cols]
#
# glb_models_lst <- list(); glb_models_df <- data.frame()
#
if (glb_is_classification && glb_is_binomial &&
(length(unique(glb_fitobs_df[, glb_rsp_var])) < 2))
stop("glb_fitobs_df$", glb_rsp_var, ": contains less than 2 unique values: ",
paste0(unique(glb_fitobs_df[, glb_rsp_var]), collapse=", "))
max_cor_y_x_vars <- orderBy(~ -cor.y.abs,
subset(glb_feats_df, (exclude.as.feat == 0) & !is.cor.y.abs.low &
is.na(cor.high.X)))[1:2, "id"]
# while(length(max_cor_y_x_vars) < 2) {
# max_cor_y_x_vars <- c(max_cor_y_x_vars, orderBy(~ -cor.y.abs,
# subset(glb_feats_df, (exclude.as.feat == 0) & !is.cor.y.abs.low))[3, "id"])
# }
if (!is.null(glb_Baseline_mdl_var)) {
if ((max_cor_y_x_vars[1] != glb_Baseline_mdl_var) &
(glb_feats_df[max_cor_y_x_vars[1], "cor.y.abs"] >
glb_feats_df[glb_Baseline_mdl_var, "cor.y.abs"]))
stop(max_cor_y_x_vars[1], " has a lower correlation with ", glb_rsp_var,
" than the Baseline var: ", glb_Baseline_mdl_var)
}
glb_model_type <- ifelse(glb_is_regression, "regression", "classification")
# Baseline
if (!is.null(glb_Baseline_mdl_var))
ret_lst <- myfit_mdl_fn(model_id="Baseline", model_method="mybaseln_classfr",
indep_vars_vctr=glb_Baseline_mdl_var,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)
# Most Frequent Outcome "MFO" model: mean(y) for regression
# Not using caret's nullModel since model stats not avl
# Cannot use rpart for multinomial classification since it predicts non-MFO
ret_lst <- myfit_mdl(model_id="MFO",
model_method=ifelse(glb_is_regression, "lm", "myMFO_classfr"),
model_type=glb_model_type,
indep_vars_vctr=".rnorm",
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)## [1] "fitting model: MFO.lm"
## [1] " indep_vars: .rnorm"
## Fitting parameter = none on full training set
##
## Call:
## lm(formula = .outcome ~ ., data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -62.833 -23.580 4.284 26.478 37.758
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 62.5402 1.3390 46.706 <2e-16 ***
## .rnorm -0.1148 1.3288 -0.086 0.931
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 31.57 on 554 degrees of freedom
## Multiple R-squared: 1.346e-05, Adjusted R-squared: -0.001792
## F-statistic: 0.00746 on 1 and 554 DF, p-value: 0.9312
##
## [1] " calling mypredict_mdl for fit:"
## [1] " calling mypredict_mdl for OOB:"
## model_id model_method feats max.nTuningRuns min.elapsedtime.everything
## 1 MFO.lm lm .rnorm 0 0.442
## min.elapsedtime.final max.R.sq.fit min.RMSE.fit max.R.sq.OOB
## 1 0.002 1.346478e-05 31.51269 NA
## min.RMSE.OOB max.Adj.R.sq.fit
## 1 NA -0.001791565if (glb_is_classification)
# "random" model - only for classification;
# none needed for regression since it is same as MFO
ret_lst <- myfit_mdl(model_id="Random", model_method="myrandom_classfr",
model_type=glb_model_type,
indep_vars_vctr=".rnorm",
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)
# Any models that have tuning parameters has "better" results with cross-validation
# (except rf) & "different" results for different outcome metrics
# Max.cor.Y
# Check impact of cv
# rpart is not a good candidate since caret does not optimize cp (only tuning parameter of rpart) well
ret_lst <- myfit_mdl(model_id="Max.cor.Y.cv.0",
model_method="rpart",
model_type=glb_model_type,
indep_vars_vctr=max_cor_y_x_vars,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df)## [1] "fitting model: Max.cor.Y.cv.0.rpart"
## [1] " indep_vars: Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr"## Loading required package: rpart## Fitting cp = 0.0758 on full training set## Loading required package: rpart.plot
## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7,
## cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2,
## surrogatestyle = 0, maxdepth = 30, xval = 0))
## n= 556
##
## CP nsplit rel error
## 1 0.0757997 0 1
##
## Node number 1: 556 observations
## mean=62.54204, MSE=993.0631
##
## n= 556
##
## node), split, n, deviance, yval
## * denotes terminal node
##
## 1) root 556 552143.1 62.54204 *
## [1] " calling mypredict_mdl for fit:"
## [1] " calling mypredict_mdl for OOB:"
## model_id model_method
## 1 Max.cor.Y.cv.0.rpart rpart
## feats max.nTuningRuns
## 1 Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr 0
## min.elapsedtime.everything min.elapsedtime.final max.R.sq.fit
## 1 0.532 0.016 0
## min.RMSE.fit max.R.sq.OOB min.RMSE.OOB
## 1 31.5129 NA NAret_lst <- myfit_mdl(model_id="Max.cor.Y.cv.0.cp.0",
model_method="rpart",
model_type=glb_model_type,
indep_vars_vctr=max_cor_y_x_vars,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=0,
tune_models_df=data.frame(parameter="cp", min=0.0, max=0.0, by=0.1))## [1] "fitting model: Max.cor.Y.cv.0.cp.0.rpart"
## [1] " indep_vars: Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr"
## Fitting cp = 0 on full training set
## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7,
## cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2,
## surrogatestyle = 0, maxdepth = 30, xval = 0))
## n= 556
##
## CP nsplit rel error
## 1 0.0757997006 0 1.0000000
## 2 0.0349025295 1 0.9242003
## 3 0.0058478990 2 0.8892978
## 4 0.0057792960 3 0.8834499
## 5 0.0005067675 4 0.8776706
## 6 0.0000000000 5 0.8771638
##
## Variable importance
## Worry.About.Info.my.fctr1 Privacy.Laws.Effective.my.fctr1
## 59 36
## Privacy.Laws.Effective.my.fctrNA.my
## 5
##
## Node number 1: 556 observations, complexity param=0.0757997
## mean=62.54204, MSE=993.0631
## left son=2 (292 obs) right son=3 (264 obs)
## Primary splits:
## Worry.About.Info.my.fctr1 < 0.5 to the left, improve=0.075799700, (0 missing)
## Privacy.Laws.Effective.my.fctr1 < 0.5 to the right, improve=0.055656000, (0 missing)
## Privacy.Laws.Effective.my.fctrNA.my < 0.5 to the right, improve=0.003566702, (0 missing)
## Surrogate splits:
## Privacy.Laws.Effective.my.fctr1 < 0.5 to the right, agree=0.556, adj=0.064, (0 split)
##
## Node number 2: 292 observations, complexity param=0.03490253
## mean=54.29244, MSE=1062.076
## left son=4 (90 obs) right son=5 (202 obs)
## Primary splits:
## Privacy.Laws.Effective.my.fctr1 < 0.5 to the right, improve=0.062139860, (0 missing)
## Privacy.Laws.Effective.my.fctrNA.my < 0.5 to the right, improve=0.001576476, (0 missing)
##
## Node number 3: 264 observations, complexity param=0.005779296
## mean=71.66659, MSE=758.1997
## left son=6 (45 obs) right son=7 (219 obs)
## Primary splits:
## Privacy.Laws.Effective.my.fctr1 < 0.5 to the right, improve=0.0159418600, (0 missing)
## Privacy.Laws.Effective.my.fctrNA.my < 0.5 to the right, improve=0.0005340128, (0 missing)
##
## Node number 4: 90 observations
## mean=42.12169, MSE=959.2431
##
## Node number 5: 202 observations, complexity param=0.005847899
## mean=59.71505, MSE=1012.49
## left son=10 (33 obs) right son=11 (169 obs)
## Primary splits:
## Privacy.Laws.Effective.my.fctrNA.my < 0.5 to the right, improve=0.01578735, (0 missing)
##
## Node number 6: 45 observations
## mean=63.99691, MSE=791.7729
##
## Node number 7: 219 observations, complexity param=0.0005067675
## mean=73.24255, MSE=736.7303
## left son=14 (15 obs) right son=15 (204 obs)
## Primary splits:
## Privacy.Laws.Effective.my.fctrNA.my < 0.5 to the right, improve=0.001734234, (0 missing)
##
## Node number 10: 33 observations
## mean=50.66739, MSE=1221.87
##
## Node number 11: 169 observations
## mean=61.48176, MSE=952.4997
##
## Node number 14: 15 observations
## mean=69.07407, MSE=867.7767
##
## Node number 15: 204 observations
## mean=73.54906, MSE=725.7229
##
## n= 556
##
## node), split, n, deviance, yval
## * denotes terminal node
##
## 1) root 556 552143.10 62.54204
## 2) Worry.About.Info.my.fctr1< 0.5 292 310126.10 54.29244
## 4) Privacy.Laws.Effective.my.fctr1>=0.5 90 86331.88 42.12169 *
## 5) Privacy.Laws.Effective.my.fctr1< 0.5 202 204523.00 59.71505
## 10) Privacy.Laws.Effective.my.fctrNA.my>=0.5 33 40321.70 50.66739 *
## 11) Privacy.Laws.Effective.my.fctrNA.my< 0.5 169 160972.40 61.48176 *
## 3) Worry.About.Info.my.fctr1>=0.5 264 200164.70 71.66659
## 6) Privacy.Laws.Effective.my.fctr1>=0.5 45 35629.78 63.99691 *
## 7) Privacy.Laws.Effective.my.fctr1< 0.5 219 161343.90 73.24255
## 14) Privacy.Laws.Effective.my.fctrNA.my>=0.5 15 13016.65 69.07407 *
## 15) Privacy.Laws.Effective.my.fctrNA.my< 0.5 204 148047.50 73.54906 *
## [1] " calling mypredict_mdl for fit:"
## [1] " calling mypredict_mdl for OOB:"
## model_id model_method
## 1 Max.cor.Y.cv.0.cp.0.rpart rpart
## feats max.nTuningRuns
## 1 Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr 0
## min.elapsedtime.everything min.elapsedtime.final max.R.sq.fit
## 1 0.466 0.015 0.1228362
## min.RMSE.fit max.R.sq.OOB min.RMSE.OOB
## 1 29.51405 NA NAif (glb_is_regression || glb_is_binomial) # For multinomials this model will be run next by default
ret_lst <- myfit_mdl(model_id="Max.cor.Y",
model_method="rpart",
model_type=glb_model_type,
indep_vars_vctr=max_cor_y_x_vars,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)## [1] "fitting model: Max.cor.Y.rpart"
## [1] " indep_vars: Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr"## Warning in nominalTrainWorkflow(x = x, y = y, wts = weights, info =
## trainInfo, : There were missing values in resampled performance measures.## Aggregating results
## Selecting tuning parameters
## Fitting cp = 0.00585 on full training set## Warning in myfit_mdl(model_id = "Max.cor.Y", model_method = "rpart",
## model_type = glb_model_type, : model's bestTune found at an extreme of
## tuneGrid for parameter: cp
## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7,
## cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2,
## surrogatestyle = 0, maxdepth = 30, xval = 0))
## n= 556
##
## CP nsplit rel error
## 1 0.075799701 0 1.0000000
## 2 0.034902530 1 0.9242003
## 3 0.005847899 2 0.8892978
##
## Variable importance
## Worry.About.Info.my.fctr1 Privacy.Laws.Effective.my.fctr1
## 66 34
##
## Node number 1: 556 observations, complexity param=0.0757997
## mean=62.54204, MSE=993.0631
## left son=2 (292 obs) right son=3 (264 obs)
## Primary splits:
## Worry.About.Info.my.fctr1 < 0.5 to the left, improve=0.075799700, (0 missing)
## Privacy.Laws.Effective.my.fctr1 < 0.5 to the right, improve=0.055656000, (0 missing)
## Privacy.Laws.Effective.my.fctrNA.my < 0.5 to the right, improve=0.003566702, (0 missing)
## Surrogate splits:
## Privacy.Laws.Effective.my.fctr1 < 0.5 to the right, agree=0.556, adj=0.064, (0 split)
##
## Node number 2: 292 observations, complexity param=0.03490253
## mean=54.29244, MSE=1062.076
## left son=4 (90 obs) right son=5 (202 obs)
## Primary splits:
## Privacy.Laws.Effective.my.fctr1 < 0.5 to the right, improve=0.062139860, (0 missing)
## Privacy.Laws.Effective.my.fctrNA.my < 0.5 to the right, improve=0.001576476, (0 missing)
##
## Node number 3: 264 observations
## mean=71.66659, MSE=758.1997
##
## Node number 4: 90 observations
## mean=42.12169, MSE=959.2431
##
## Node number 5: 202 observations
## mean=59.71505, MSE=1012.49
##
## n= 556
##
## node), split, n, deviance, yval
## * denotes terminal node
##
## 1) root 556 552143.10 62.54204
## 2) Worry.About.Info.my.fctr1< 0.5 292 310126.10 54.29244
## 4) Privacy.Laws.Effective.my.fctr1>=0.5 90 86331.88 42.12169 *
## 5) Privacy.Laws.Effective.my.fctr1< 0.5 202 204523.00 59.71505 *
## 3) Worry.About.Info.my.fctr1>=0.5 264 200164.70 71.66659 *
## [1] " calling mypredict_mdl for fit:"
## [1] " calling mypredict_mdl for OOB:"
## model_id model_method
## 1 Max.cor.Y.rpart rpart
## feats max.nTuningRuns
## 1 Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr 3
## min.elapsedtime.everything min.elapsedtime.final max.R.sq.fit
## 1 0.947 0.016 0.1107022
## min.RMSE.fit max.R.sq.OOB min.RMSE.OOB max.Rsquared.fit min.RMSESD.fit
## 1 29.87947 NA NA 0.1033123 0.8361541
## max.RsquaredSD.fit
## 1 0.02379652# Used to compare vs. Interactions.High.cor.Y and/or Max.cor.Y.TmSrs
ret_lst <- myfit_mdl(model_id="Max.cor.Y",
model_method=ifelse(glb_is_regression, "lm",
ifelse(glb_is_binomial, "glm", "rpart")),
model_type=glb_model_type,
indep_vars_vctr=max_cor_y_x_vars,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)## [1] "fitting model: Max.cor.Y.lm"
## [1] " indep_vars: Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr"
## Aggregating results
## Fitting final model on full training set
## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced
##
## Call:
## lm(formula = .outcome ~ ., data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -74.720 -22.506 3.058 25.280 55.470
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 60.068 2.082 28.850 < 2e-16
## Worry.About.Info.my.fctr1 14.652 2.573 5.694 2.02e-08
## Worry.About.Info.my.fctrNA.my -52.944 29.960 -1.767 0.0778
## Privacy.Laws.Effective.my.fctr1 -15.539 3.027 -5.134 3.95e-07
## Privacy.Laws.Effective.my.fctrNA.my -7.124 4.624 -1.541 0.1240
##
## (Intercept) ***
## Worry.About.Info.my.fctr1 ***
## Worry.About.Info.my.fctrNA.my .
## Privacy.Laws.Effective.my.fctr1 ***
## Privacy.Laws.Effective.my.fctrNA.my
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 29.63 on 551 degrees of freedom
## Multiple R-squared: 0.1236, Adjusted R-squared: 0.1172
## F-statistic: 19.43 on 4 and 551 DF, p-value: 5.761e-15
##
## [1] " calling mypredict_mdl for fit:"
## [1] " calling mypredict_mdl for OOB:"
## model_id model_method
## 1 Max.cor.Y.lm lm
## feats max.nTuningRuns
## 1 Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr 1
## min.elapsedtime.everything min.elapsedtime.final max.R.sq.fit
## 1 0.841 0.004 0.1235906
## min.RMSE.fit max.R.sq.OOB min.RMSE.OOB max.Adj.R.sq.fit max.Rsquared.fit
## 1 29.77477 NA NA 0.1172283 0.1089247
## min.RMSESD.fit max.RsquaredSD.fit
## 1 0.8402025 0.01758807if (!is.null(glb_date_vars) &&
(sum(grepl(paste(glb_date_vars, "\\.day\\.minutes\\.poly\\.", sep=""),
names(glb_allobs_df))) > 0)) {
# ret_lst <- myfit_mdl(model_id="Max.cor.Y.TmSrs.poly1",
# model_method=ifelse(glb_is_regression, "lm",
# ifelse(glb_is_binomial, "glm", "rpart")),
# model_type=glb_model_type,
# indep_vars_vctr=c(max_cor_y_x_vars, paste0(glb_date_vars, ".day.minutes")),
# rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
# fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
# n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)
#
ret_lst <- myfit_mdl(model_id="Max.cor.Y.TmSrs.poly",
model_method=ifelse(glb_is_regression, "lm",
ifelse(glb_is_binomial, "glm", "rpart")),
model_type=glb_model_type,
indep_vars_vctr=c(max_cor_y_x_vars,
grep(paste(glb_date_vars, "\\.day\\.minutes\\.poly\\.", sep=""),
names(glb_allobs_df), value=TRUE)),
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)
}
# Interactions.High.cor.Y
if (length(int_feats <- setdiff(unique(glb_feats_df$cor.high.X), NA)) > 0) {
# lm & glm handle interaction terms; rpart & rf do not
if (glb_is_regression || glb_is_binomial) {
indep_vars_vctr <-
c(max_cor_y_x_vars, paste(max_cor_y_x_vars[1], int_feats, sep=":"))
} else { indep_vars_vctr <- union(max_cor_y_x_vars, int_feats) }
ret_lst <- myfit_mdl(model_id="Interact.High.cor.Y",
model_method=ifelse(glb_is_regression, "lm",
ifelse(glb_is_binomial, "glm", "rpart")),
model_type=glb_model_type,
indep_vars_vctr,
glb_rsp_var, glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)
}
# Low.cor.X
# if (glb_is_classification && glb_is_binomial)
# indep_vars_vctr <- subset(glb_feats_df, is.na(cor.high.X) &
# is.ConditionalX.y &
# (exclude.as.feat != 1))[, "id"] else
indep_vars_vctr <- subset(glb_feats_df, is.na(cor.high.X) & !myNearZV &
(exclude.as.feat != 1))[, "id"]
myadjust_interaction_feats <- function(vars_vctr) {
for (feat in subset(glb_feats_df, !is.na(interaction.feat))$id)
if (feat %in% vars_vctr)
vars_vctr <- union(setdiff(vars_vctr, feat),
paste0(glb_feats_df[glb_feats_df$id == feat, "interaction.feat"], ":", feat))
return(vars_vctr)
}
indep_vars_vctr <- myadjust_interaction_feats(indep_vars_vctr)
ret_lst <- myfit_mdl(model_id="Low.cor.X",
model_method=ifelse(glb_is_regression, "lm",
ifelse(glb_is_binomial, "glm", "rpart")),
indep_vars_vctr=indep_vars_vctr,
model_type=glb_model_type,
glb_rsp_var, glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=NULL)## [1] "fitting model: Low.cor.X.lm"
## [1] " indep_vars: Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr"
## Aggregating results
## Fitting final model on full training set
## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced##
## Call:
## lm(formula = .outcome ~ ., data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -76.048 -19.249 4.149 21.387 65.612
##
## Coefficients: (1 not defined because of singularities)
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 34.9170 12.4594 2.802 0.00526
## Worry.About.Info.my.fctr1 13.7799 2.6606 5.179 3.20e-07
## Worry.About.Info.my.fctrNA.my -57.2029 30.1759 -1.896 0.05856
## `Age.my.fctr(33.6,49.2]` 11.0518 3.7471 2.949 0.00333
## `Age.my.fctr(49.2,64.8]` 10.9517 3.4654 3.160 0.00167
## `Age.my.fctr(64.8,80.4]` 1.8203 4.3536 0.418 0.67604
## `Age.my.fctr(80.4,96.1]` 2.4955 9.2478 0.270 0.78738
## Age.my.fctrNA.my 14.7688 8.7521 1.687 0.09212
## Tried.Masking.Identity.my.fctr1 4.6212 3.5949 1.285 0.19920
## Tried.Masking.Identity.my.fctrNA.my -6.8003 13.4700 -0.505 0.61388
## Internet.Use.my 17.9850 9.8992 1.817 0.06982
## Sex.fctrFemale 2.2626 2.6248 0.862 0.38909
## Conservativeness.my.fctr2 0.8528 6.4467 0.132 0.89481
## Conservativeness.my.fctr3 5.3331 5.9749 0.893 0.37249
## Conservativeness.my.fctr4 4.5422 5.9929 0.758 0.44884
## Conservativeness.my.fctr5 3.9890 7.0603 0.565 0.57232
## Conservativeness.my.fctrNA.my 5.1013 7.9028 0.646 0.51888
## Smartphone.my.fctr1 2.6720 2.9600 0.903 0.36709
## Smartphone.my.fctrNA.my 0.6564 8.4128 0.078 0.93784
## .rnorm -0.1930 1.2831 -0.150 0.88049
## Info.On.Internet.my.fctr1 -0.7005 5.4397 -0.129 0.89759
## Info.On.Internet.my.fctr10 -20.7025 10.8093 -1.915 0.05601
## Info.On.Internet.my.fctr11 16.5327 13.7849 1.199 0.23095
## Info.On.Internet.my.fctr2 -10.2710 5.0344 -2.040 0.04184
## Info.On.Internet.my.fctr3 -7.8068 5.1808 -1.507 0.13245
## Info.On.Internet.my.fctr4 -8.5032 5.0476 -1.685 0.09267
## Info.On.Internet.my.fctr5 -6.3418 5.4519 -1.163 0.24527
## Info.On.Internet.my.fctr6 -7.9571 5.8301 -1.365 0.17290
## Info.On.Internet.my.fctr7 -9.1325 5.8907 -1.550 0.12167
## Info.On.Internet.my.fctr8 4.3286 6.6599 0.650 0.51602
## Info.On.Internet.my.fctr9 -7.5259 9.1857 -0.819 0.41299
## Info.On.Internet.my.fctrNA.my NA NA NA NA
## Region.fctrSouth 2.2245 4.0273 0.552 0.58094
## Region.fctrWest 0.1380 4.2571 0.032 0.97414
## Region.fctrMidwest -0.2835 4.3720 -0.065 0.94832
## Anonymity.Possible.my.fctr1 -3.8693 2.6915 -1.438 0.15115
## Anonymity.Possible.my.fctrNA.my 1.9033 6.1261 0.311 0.75617
## Privacy.Laws.Effective.my.fctr1 -14.8815 3.1009 -4.799 2.09e-06
## Privacy.Laws.Effective.my.fctrNA.my -6.7398 4.7663 -1.414 0.15795
##
## (Intercept) **
## Worry.About.Info.my.fctr1 ***
## Worry.About.Info.my.fctrNA.my .
## `Age.my.fctr(33.6,49.2]` **
## `Age.my.fctr(49.2,64.8]` **
## `Age.my.fctr(64.8,80.4]`
## `Age.my.fctr(80.4,96.1]`
## Age.my.fctrNA.my .
## Tried.Masking.Identity.my.fctr1
## Tried.Masking.Identity.my.fctrNA.my
## Internet.Use.my .
## Sex.fctrFemale
## Conservativeness.my.fctr2
## Conservativeness.my.fctr3
## Conservativeness.my.fctr4
## Conservativeness.my.fctr5
## Conservativeness.my.fctrNA.my
## Smartphone.my.fctr1
## Smartphone.my.fctrNA.my
## .rnorm
## Info.On.Internet.my.fctr1
## Info.On.Internet.my.fctr10 .
## Info.On.Internet.my.fctr11
## Info.On.Internet.my.fctr2 *
## Info.On.Internet.my.fctr3
## Info.On.Internet.my.fctr4 .
## Info.On.Internet.my.fctr5
## Info.On.Internet.my.fctr6
## Info.On.Internet.my.fctr7
## Info.On.Internet.my.fctr8
## Info.On.Internet.my.fctr9
## Info.On.Internet.my.fctrNA.my
## Region.fctrSouth
## Region.fctrWest
## Region.fctrMidwest
## Anonymity.Possible.my.fctr1
## Anonymity.Possible.my.fctrNA.my
## Privacy.Laws.Effective.my.fctr1 ***
## Privacy.Laws.Effective.my.fctrNA.my
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 29.24 on 518 degrees of freedom
## Multiple R-squared: 0.1977, Adjusted R-squared: 0.1404
## F-statistic: 3.449 on 37 and 518 DF, p-value: 2.31e-10
##
## [1] " calling mypredict_mdl for fit:"## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading## [1] " calling mypredict_mdl for OOB:"## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading
## model_id model_method
## 1 Low.cor.X.lm lm
## feats
## 1 Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 1 0.983 0.015
## max.R.sq.fit min.RMSE.fit max.R.sq.OOB min.RMSE.OOB max.Adj.R.sq.fit
## 1 0.1976727 31.31739 NA NA 0.1403636
## max.Rsquared.fit min.RMSESD.fit max.RsquaredSD.fit
## 1 0.07528015 1.469406 0.02687989rm(ret_lst)
glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 10 fit.models 7 0 20.175 32.709 12.535
## 11 fit.models 7 1 32.710 NA NAfit.models_1_chunk_df <- myadd_chunk(NULL, "fit.models_1_bgn")## label step_major step_minor bgn end elapsed
## 1 fit.models_1_bgn 1 0 34.331 NA NA# Options:
# 1. rpart & rf manual tuning
# 2. rf without pca (default: with pca)
#stop(here); sav_models_lst <- glb_models_lst; sav_models_df <- glb_models_df
#glb_models_lst <- sav_models_lst; glb_models_df <- sav_models_df
# All X that is not user excluded
# if (glb_is_classification && glb_is_binomial) {
# model_id_pfx <- "Conditional.X"
# # indep_vars_vctr <- setdiff(names(glb_fitobs_df), union(glb_rsp_var, glb_exclude_vars_as_features))
# indep_vars_vctr <- subset(glb_feats_df, is.ConditionalX.y &
# (exclude.as.feat != 1))[, "id"]
# } else {
model_id_pfx <- "All.X"
indep_vars_vctr <- subset(glb_feats_df, !myNearZV &
(exclude.as.feat != 1))[, "id"]
# }
indep_vars_vctr <- myadjust_interaction_feats(indep_vars_vctr)
for (method in glb_models_method_vctr) {
fit.models_1_chunk_df <- myadd_chunk(fit.models_1_chunk_df,
paste0("fit.models_1_", method), major.inc=TRUE)
if (method %in% c("rpart", "rf")) {
# rpart: fubar's the tree
# rf: skip the scenario w/ .rnorm for speed
indep_vars_vctr <- setdiff(indep_vars_vctr, c(".rnorm"))
model_id <- paste0(model_id_pfx, ".no.rnorm")
} else model_id <- model_id_pfx
if (method %in% c("glm")) # for a "robust" glm model
indep_vars_vctr <- setdiff(indep_vars_vctr, c(NULL
,"A.nchrs.log" # correlated to "S.*"
,"A.ndgts.log" # correlated to "S.*"
,"A.nuppr.log" # correlated to "S.*"
,"A.npnct01.log" # identical to "S.npnct01.log"
,"A.npnct03.log" # correlated to "S.npnct03.log"
,"A.npnct04.log" # correlated to "S.npnct04.log"
,"A.npnct06.log" # identical to "S.npnct06.log"
,"A.npnct07.log" # identical to "S.npnct07.log"
,"A.npnct08.log" # correlated to "S.npnct08.log"
,"A.npnct11.log" # correlated to "S.*"
,"A.npnct12.log" # correlated to "S.*"
,"S.npnct14.log" # correlated to "A.*"
,"A.npnct15.log" # correlated to "S.npnct15.log"
,"A.npnct16.log" # correlated to "S.npnct16.log"
,"A.npnct19.log" # correlated to "S.*"
,"A.npnct20.log" # identical to "S.npnct20.log"
,"A.npnct21.log" # correlated to "S.npnct21.log"
,"A.P.daily.clip.report" # identical to "S.*"
,"S.P.daily.clip.report" # identical to "H.*"
,"A.P.http" # correlated to "A.npnct14.log"
,"A.P.fashion.week" # identical to "S.*"
,"H.P.first.draft" # correlated to "H.T.first"
,"A.P.first.draft" # identical to "S.*"
,"A.P.metropolitan.diary.colon" # identical to "S.*"
,"A.P.year.colon" # identical to "S.P.year.colon"
))
ret_lst <- myfit_mdl(model_id=model_id, model_method=method,
indep_vars_vctr=indep_vars_vctr,
model_type=glb_model_type,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
n_cv_folds=glb_n_cv_folds, tune_models_df=glb_tune_models_df)
# If All.X.glm is less accurate than Low.Cor.X.glm
# check NA coefficients & filter appropriate terms in indep_vars_vctr
# if (method == "glm") {
# orig_glm <- glb_models_lst[[paste0(model_id, ".", model_method)]]$finalModel
# orig_glm <- glb_models_lst[["All.X.glm"]]$finalModel; print(summary(orig_glm))
# vif_orig_glm <- vif(orig_glm); print(vif_orig_glm)
# print(vif_orig_glm[!is.na(vif_orig_glm) & (vif_orig_glm == Inf)])
# print(which.max(vif_orig_glm))
# print(sort(vif_orig_glm[vif_orig_glm >= 1.0e+03], decreasing=TRUE))
# glb_fitobs_df[c(1143, 3637, 3953, 4105), c("UniqueID", "Popular", "H.P.quandary", "Headline")]
# glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.nchrs.log", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in% grep("[HSA]\\.nchrs.log", glb_feats_df$id, value=TRUE), ]
# glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.npnct14.log", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in% grep("[HSA]\\.npnct14.log", glb_feats_df$id, value=TRUE), ]
# glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.T.scen", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in% grep("[HSA]\\.T.scen", glb_feats_df$id, value=TRUE), ]
# glb_feats_df[glb_feats_df$id %in% grep("[HSA]\\.P.first", glb_feats_df$id, value=TRUE) | glb_feats_df$cor.high.X %in% grep("[HSA]\\.P.first", glb_feats_df$id, value=TRUE), ]
# all.equal(glb_allobs_df$S.nuppr.log, glb_allobs_df$A.nuppr.log)
# all.equal(glb_allobs_df$S.npnct19.log, glb_allobs_df$A.npnct19.log)
# all.equal(glb_allobs_df$S.P.year.colon, glb_allobs_df$A.P.year.colon)
# all.equal(glb_allobs_df$S.T.share, glb_allobs_df$A.T.share)
# all.equal(glb_allobs_df$H.T.clip, glb_allobs_df$H.P.daily.clip.report)
# cor(glb_allobs_df$S.T.herald, glb_allobs_df$S.T.tribun)
# dsp_obs(Abstract.contains="[Dd]iar", cols=("Abstract"), all=TRUE)
# dsp_obs(Abstract.contains="[Ss]hare", cols=("Abstract"), all=TRUE)
# subset(glb_feats_df, cor.y.abs <= glb_feats_df[glb_feats_df$id == ".rnorm", "cor.y.abs"])
# corxx_mtrx <- cor(data.matrix(glb_allobs_df[, setdiff(names(glb_allobs_df), myfind_chr_cols_df(glb_allobs_df))]), use="pairwise.complete.obs"); abs_corxx_mtrx <- abs(corxx_mtrx); diag(abs_corxx_mtrx) <- 0
# which.max(abs_corxx_mtrx["S.T.tribun", ])
# abs_corxx_mtrx["A.npnct08.log", "S.npnct08.log"]
# step_glm <- step(orig_glm)
# }
# Since caret does not optimize rpart well
# if (method == "rpart")
# ret_lst <- myfit_mdl(model_id=paste0(model_id_pfx, ".cp.0"), model_method=method,
# indep_vars_vctr=indep_vars_vctr,
# model_type=glb_model_type,
# rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
# fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
# n_cv_folds=0, tune_models_df=data.frame(parameter="cp", min=0.0, max=0.0, by=0.1))
}## label step_major step_minor bgn end elapsed
## 1 fit.models_1_bgn 1 0 34.331 34.345 0.014
## 2 fit.models_1_lm 2 0 34.345 NA NA
## [1] "fitting model: All.X.lm"
## [1] " indep_vars: Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr"
## Aggregating results
## Fitting final model on full training set
## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced##
## Call:
## lm(formula = .outcome ~ ., data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -76.048 -19.249 4.149 21.387 65.612
##
## Coefficients: (1 not defined because of singularities)
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 34.9170 12.4594 2.802 0.00526
## Worry.About.Info.my.fctr1 13.7799 2.6606 5.179 3.20e-07
## Worry.About.Info.my.fctrNA.my -57.2029 30.1759 -1.896 0.05856
## `Age.my.fctr(33.6,49.2]` 11.0518 3.7471 2.949 0.00333
## `Age.my.fctr(49.2,64.8]` 10.9517 3.4654 3.160 0.00167
## `Age.my.fctr(64.8,80.4]` 1.8203 4.3536 0.418 0.67604
## `Age.my.fctr(80.4,96.1]` 2.4955 9.2478 0.270 0.78738
## Age.my.fctrNA.my 14.7688 8.7521 1.687 0.09212
## Tried.Masking.Identity.my.fctr1 4.6212 3.5949 1.285 0.19920
## Tried.Masking.Identity.my.fctrNA.my -6.8003 13.4700 -0.505 0.61388
## Internet.Use.my 17.9850 9.8992 1.817 0.06982
## Sex.fctrFemale 2.2626 2.6248 0.862 0.38909
## Conservativeness.my.fctr2 0.8528 6.4467 0.132 0.89481
## Conservativeness.my.fctr3 5.3331 5.9749 0.893 0.37249
## Conservativeness.my.fctr4 4.5422 5.9929 0.758 0.44884
## Conservativeness.my.fctr5 3.9890 7.0603 0.565 0.57232
## Conservativeness.my.fctrNA.my 5.1013 7.9028 0.646 0.51888
## Smartphone.my.fctr1 2.6720 2.9600 0.903 0.36709
## Smartphone.my.fctrNA.my 0.6564 8.4128 0.078 0.93784
## .rnorm -0.1930 1.2831 -0.150 0.88049
## Info.On.Internet.my.fctr1 -0.7005 5.4397 -0.129 0.89759
## Info.On.Internet.my.fctr10 -20.7025 10.8093 -1.915 0.05601
## Info.On.Internet.my.fctr11 16.5327 13.7849 1.199 0.23095
## Info.On.Internet.my.fctr2 -10.2710 5.0344 -2.040 0.04184
## Info.On.Internet.my.fctr3 -7.8068 5.1808 -1.507 0.13245
## Info.On.Internet.my.fctr4 -8.5032 5.0476 -1.685 0.09267
## Info.On.Internet.my.fctr5 -6.3418 5.4519 -1.163 0.24527
## Info.On.Internet.my.fctr6 -7.9571 5.8301 -1.365 0.17290
## Info.On.Internet.my.fctr7 -9.1325 5.8907 -1.550 0.12167
## Info.On.Internet.my.fctr8 4.3286 6.6599 0.650 0.51602
## Info.On.Internet.my.fctr9 -7.5259 9.1857 -0.819 0.41299
## Info.On.Internet.my.fctrNA.my NA NA NA NA
## Region.fctrSouth 2.2245 4.0273 0.552 0.58094
## Region.fctrWest 0.1380 4.2571 0.032 0.97414
## Region.fctrMidwest -0.2835 4.3720 -0.065 0.94832
## Anonymity.Possible.my.fctr1 -3.8693 2.6915 -1.438 0.15115
## Anonymity.Possible.my.fctrNA.my 1.9033 6.1261 0.311 0.75617
## Privacy.Laws.Effective.my.fctr1 -14.8815 3.1009 -4.799 2.09e-06
## Privacy.Laws.Effective.my.fctrNA.my -6.7398 4.7663 -1.414 0.15795
##
## (Intercept) **
## Worry.About.Info.my.fctr1 ***
## Worry.About.Info.my.fctrNA.my .
## `Age.my.fctr(33.6,49.2]` **
## `Age.my.fctr(49.2,64.8]` **
## `Age.my.fctr(64.8,80.4]`
## `Age.my.fctr(80.4,96.1]`
## Age.my.fctrNA.my .
## Tried.Masking.Identity.my.fctr1
## Tried.Masking.Identity.my.fctrNA.my
## Internet.Use.my .
## Sex.fctrFemale
## Conservativeness.my.fctr2
## Conservativeness.my.fctr3
## Conservativeness.my.fctr4
## Conservativeness.my.fctr5
## Conservativeness.my.fctrNA.my
## Smartphone.my.fctr1
## Smartphone.my.fctrNA.my
## .rnorm
## Info.On.Internet.my.fctr1
## Info.On.Internet.my.fctr10 .
## Info.On.Internet.my.fctr11
## Info.On.Internet.my.fctr2 *
## Info.On.Internet.my.fctr3
## Info.On.Internet.my.fctr4 .
## Info.On.Internet.my.fctr5
## Info.On.Internet.my.fctr6
## Info.On.Internet.my.fctr7
## Info.On.Internet.my.fctr8
## Info.On.Internet.my.fctr9
## Info.On.Internet.my.fctrNA.my
## Region.fctrSouth
## Region.fctrWest
## Region.fctrMidwest
## Anonymity.Possible.my.fctr1
## Anonymity.Possible.my.fctrNA.my
## Privacy.Laws.Effective.my.fctr1 ***
## Privacy.Laws.Effective.my.fctrNA.my
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 29.24 on 518 degrees of freedom
## Multiple R-squared: 0.1977, Adjusted R-squared: 0.1404
## F-statistic: 3.449 on 37 and 518 DF, p-value: 2.31e-10
##
## [1] " calling mypredict_mdl for fit:"## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading## [1] " calling mypredict_mdl for OOB:"## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading
## model_id model_method
## 1 All.X.lm lm
## feats
## 1 Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 1 0.906 0.015
## max.R.sq.fit min.RMSE.fit max.R.sq.OOB min.RMSE.OOB max.Adj.R.sq.fit
## 1 0.1976727 31.31739 NA NA 0.1403636
## max.Rsquared.fit min.RMSESD.fit max.RsquaredSD.fit
## 1 0.07528015 1.469406 0.02687989
## label step_major step_minor bgn end elapsed
## 2 fit.models_1_lm 2 0 34.345 36.768 2.423
## 3 fit.models_1_glm 3 0 36.768 NA NA
## [1] "fitting model: All.X.glm"
## [1] " indep_vars: Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr"
## Aggregating results
## Fitting final model on full training set
## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced##
## Call:
## NULL
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -76.048 -19.249 4.149 21.387 65.612
##
## Coefficients: (1 not defined because of singularities)
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 34.9170 12.4594 2.802 0.00526
## Worry.About.Info.my.fctr1 13.7799 2.6606 5.179 3.20e-07
## Worry.About.Info.my.fctrNA.my -57.2029 30.1759 -1.896 0.05856
## `Age.my.fctr(33.6,49.2]` 11.0518 3.7471 2.949 0.00333
## `Age.my.fctr(49.2,64.8]` 10.9517 3.4654 3.160 0.00167
## `Age.my.fctr(64.8,80.4]` 1.8203 4.3536 0.418 0.67604
## `Age.my.fctr(80.4,96.1]` 2.4955 9.2478 0.270 0.78738
## Age.my.fctrNA.my 14.7688 8.7521 1.687 0.09212
## Tried.Masking.Identity.my.fctr1 4.6212 3.5949 1.285 0.19920
## Tried.Masking.Identity.my.fctrNA.my -6.8003 13.4700 -0.505 0.61388
## Internet.Use.my 17.9850 9.8992 1.817 0.06982
## Sex.fctrFemale 2.2626 2.6248 0.862 0.38909
## Conservativeness.my.fctr2 0.8528 6.4467 0.132 0.89481
## Conservativeness.my.fctr3 5.3331 5.9749 0.893 0.37249
## Conservativeness.my.fctr4 4.5422 5.9929 0.758 0.44884
## Conservativeness.my.fctr5 3.9890 7.0603 0.565 0.57232
## Conservativeness.my.fctrNA.my 5.1013 7.9028 0.646 0.51888
## Smartphone.my.fctr1 2.6720 2.9600 0.903 0.36709
## Smartphone.my.fctrNA.my 0.6564 8.4128 0.078 0.93784
## .rnorm -0.1930 1.2831 -0.150 0.88049
## Info.On.Internet.my.fctr1 -0.7005 5.4397 -0.129 0.89759
## Info.On.Internet.my.fctr10 -20.7025 10.8093 -1.915 0.05601
## Info.On.Internet.my.fctr11 16.5327 13.7849 1.199 0.23095
## Info.On.Internet.my.fctr2 -10.2710 5.0344 -2.040 0.04184
## Info.On.Internet.my.fctr3 -7.8068 5.1808 -1.507 0.13245
## Info.On.Internet.my.fctr4 -8.5032 5.0476 -1.685 0.09267
## Info.On.Internet.my.fctr5 -6.3418 5.4519 -1.163 0.24527
## Info.On.Internet.my.fctr6 -7.9571 5.8301 -1.365 0.17290
## Info.On.Internet.my.fctr7 -9.1325 5.8907 -1.550 0.12167
## Info.On.Internet.my.fctr8 4.3286 6.6599 0.650 0.51602
## Info.On.Internet.my.fctr9 -7.5259 9.1857 -0.819 0.41299
## Info.On.Internet.my.fctrNA.my NA NA NA NA
## Region.fctrSouth 2.2245 4.0273 0.552 0.58094
## Region.fctrWest 0.1380 4.2571 0.032 0.97414
## Region.fctrMidwest -0.2835 4.3720 -0.065 0.94832
## Anonymity.Possible.my.fctr1 -3.8693 2.6915 -1.438 0.15115
## Anonymity.Possible.my.fctrNA.my 1.9033 6.1261 0.311 0.75617
## Privacy.Laws.Effective.my.fctr1 -14.8815 3.1009 -4.799 2.09e-06
## Privacy.Laws.Effective.my.fctrNA.my -6.7398 4.7663 -1.414 0.15795
##
## (Intercept) **
## Worry.About.Info.my.fctr1 ***
## Worry.About.Info.my.fctrNA.my .
## `Age.my.fctr(33.6,49.2]` **
## `Age.my.fctr(49.2,64.8]` **
## `Age.my.fctr(64.8,80.4]`
## `Age.my.fctr(80.4,96.1]`
## Age.my.fctrNA.my .
## Tried.Masking.Identity.my.fctr1
## Tried.Masking.Identity.my.fctrNA.my
## Internet.Use.my .
## Sex.fctrFemale
## Conservativeness.my.fctr2
## Conservativeness.my.fctr3
## Conservativeness.my.fctr4
## Conservativeness.my.fctr5
## Conservativeness.my.fctrNA.my
## Smartphone.my.fctr1
## Smartphone.my.fctrNA.my
## .rnorm
## Info.On.Internet.my.fctr1
## Info.On.Internet.my.fctr10 .
## Info.On.Internet.my.fctr11
## Info.On.Internet.my.fctr2 *
## Info.On.Internet.my.fctr3
## Info.On.Internet.my.fctr4 .
## Info.On.Internet.my.fctr5
## Info.On.Internet.my.fctr6
## Info.On.Internet.my.fctr7
## Info.On.Internet.my.fctr8
## Info.On.Internet.my.fctr9
## Info.On.Internet.my.fctrNA.my
## Region.fctrSouth
## Region.fctrWest
## Region.fctrMidwest
## Anonymity.Possible.my.fctr1
## Anonymity.Possible.my.fctrNA.my
## Privacy.Laws.Effective.my.fctr1 ***
## Privacy.Laws.Effective.my.fctrNA.my
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for gaussian family taken to be 855.2114)
##
## Null deviance: 552143 on 555 degrees of freedom
## Residual deviance: 442999 on 518 degrees of freedom
## AIC: 5370.2
##
## Number of Fisher Scoring iterations: 2
##
## [1] " calling mypredict_mdl for fit:"## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading## [1] " calling mypredict_mdl for OOB:"## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading## model_id model_method
## 1 All.X.glm glm
## feats
## 1 Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 1 0.977 0.067
## max.R.sq.fit min.RMSE.fit max.R.sq.OOB min.RMSE.OOB min.aic.fit
## 1 0.1976727 31.31739 NA NA 5370.249
## max.Rsquared.fit min.RMSESD.fit max.RsquaredSD.fit
## 1 0.07528015 1.469406 0.02687989
## label step_major step_minor bgn end elapsed
## 3 fit.models_1_glm 3 0 36.768 39.446 2.678
## 4 fit.models_1_bayesglm 4 0 39.446 NA NA
## [1] "fitting model: All.X.bayesglm"
## [1] " indep_vars: Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr"## Loading required package: arm
## Loading required package: MASS
##
## Attaching package: 'MASS'
##
## The following object is masked from 'package:dplyr':
##
## select
##
## Loading required package: Matrix
## Loading required package: lme4
## Loading required package: Rcpp
##
## Attaching package: 'lme4'
##
## The following object is masked from 'package:nlme':
##
## lmList
##
##
## arm (Version 1.8-5, built: 2015-05-13)
##
## Working directory is /Users/bbalaji-2012/Documents/Work/Courses/MIT/Analytics_Edge_15_071x/Assignments/HW1_Pew_Anonymity## Aggregating results
## Fitting final model on full training set
##
## Call:
## NULL
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -75.98 -19.29 4.22 21.42 65.50
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 35.0459 12.4214 2.821 0.00497
## Worry.About.Info.my.fctr1 13.7815 2.6619 5.177 3.23e-07
## Worry.About.Info.my.fctrNA.my -53.8001 29.2871 -1.837 0.06679
## `Age.my.fctr(33.6,49.2]` 11.0295 3.7464 2.944 0.00339
## `Age.my.fctr(49.2,64.8]` 10.9181 3.4641 3.152 0.00172
## `Age.my.fctr(64.8,80.4]` 1.8000 4.3514 0.414 0.67929
## `Age.my.fctr(80.4,96.1]` 2.4664 9.2236 0.267 0.78926
## Age.my.fctrNA.my 14.7009 8.7317 1.684 0.09286
## Tried.Masking.Identity.my.fctr1 4.6089 3.5960 1.282 0.20053
## Tried.Masking.Identity.my.fctrNA.my -6.7242 13.3854 -0.502 0.61563
## Internet.Use.my 17.8089 9.8665 1.805 0.07166
## Sex.fctrFemale 2.2844 2.6259 0.870 0.38474
## Conservativeness.my.fctr2 0.7745 6.4167 0.121 0.90398
## Conservativeness.my.fctr3 5.2966 5.9457 0.891 0.37343
## Conservativeness.my.fctr4 4.5163 5.9637 0.757 0.44922
## Conservativeness.my.fctr5 3.9506 7.0301 0.562 0.57439
## Conservativeness.my.fctrNA.my 5.0581 7.8700 0.643 0.52070
## Smartphone.my.fctr1 2.6593 2.9596 0.899 0.36931
## Smartphone.my.fctrNA.my 0.6621 8.3961 0.079 0.93718
## .rnorm -0.1916 1.2839 -0.149 0.88142
## Info.On.Internet.my.fctr1 -0.6843 5.4239 -0.126 0.89965
## Info.On.Internet.my.fctr10 -20.4873 10.7602 -1.904 0.05747
## Info.On.Internet.my.fctr11 16.3989 13.6899 1.198 0.23151
## Info.On.Internet.my.fctr2 -10.1889 5.0189 -2.030 0.04286
## Info.On.Internet.my.fctr3 -7.7262 5.1648 -1.496 0.13528
## Info.On.Internet.my.fctr4 -8.4232 5.0321 -1.674 0.09476
## Info.On.Internet.my.fctr5 -6.2591 5.4346 -1.152 0.24997
## Info.On.Internet.my.fctr6 -7.8700 5.8120 -1.354 0.17629
## Info.On.Internet.my.fctr7 -9.0423 5.8731 -1.540 0.12427
## Info.On.Internet.my.fctr8 4.3869 6.6399 0.661 0.50911
## Info.On.Internet.my.fctr9 -7.4100 9.1526 -0.810 0.41854
## Info.On.Internet.my.fctrNA.my 0.0000 157.8871 0.000 1.00000
## Region.fctrSouth 2.2574 4.0245 0.561 0.57509
## Region.fctrWest 0.1721 4.2542 0.040 0.96774
## Region.fctrMidwest -0.2539 4.3694 -0.058 0.95368
## Anonymity.Possible.my.fctr1 -3.8571 2.6929 -1.432 0.15266
## Anonymity.Possible.my.fctrNA.my 1.9082 6.1221 0.312 0.75541
## Privacy.Laws.Effective.my.fctr1 -14.8770 3.1023 -4.796 2.13e-06
## Privacy.Laws.Effective.my.fctrNA.my -6.7867 4.7639 -1.425 0.15488
##
## (Intercept) **
## Worry.About.Info.my.fctr1 ***
## Worry.About.Info.my.fctrNA.my .
## `Age.my.fctr(33.6,49.2]` **
## `Age.my.fctr(49.2,64.8]` **
## `Age.my.fctr(64.8,80.4]`
## `Age.my.fctr(80.4,96.1]`
## Age.my.fctrNA.my .
## Tried.Masking.Identity.my.fctr1
## Tried.Masking.Identity.my.fctrNA.my
## Internet.Use.my .
## Sex.fctrFemale
## Conservativeness.my.fctr2
## Conservativeness.my.fctr3
## Conservativeness.my.fctr4
## Conservativeness.my.fctr5
## Conservativeness.my.fctrNA.my
## Smartphone.my.fctr1
## Smartphone.my.fctrNA.my
## .rnorm
## Info.On.Internet.my.fctr1
## Info.On.Internet.my.fctr10 .
## Info.On.Internet.my.fctr11
## Info.On.Internet.my.fctr2 *
## Info.On.Internet.my.fctr3
## Info.On.Internet.my.fctr4 .
## Info.On.Internet.my.fctr5
## Info.On.Internet.my.fctr6
## Info.On.Internet.my.fctr7
## Info.On.Internet.my.fctr8
## Info.On.Internet.my.fctr9
## Info.On.Internet.my.fctrNA.my
## Region.fctrSouth
## Region.fctrWest
## Region.fctrMidwest
## Anonymity.Possible.my.fctr1
## Anonymity.Possible.my.fctrNA.my
## Privacy.Laws.Effective.my.fctr1 ***
## Privacy.Laws.Effective.my.fctrNA.my
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for gaussian family taken to be 856.889)
##
## Null deviance: 552143 on 555 degrees of freedom
## Residual deviance: 443012 on 517 degrees of freedom
## AIC: 5372.3
##
## Number of Fisher Scoring iterations: 8
##
## [1] " calling mypredict_mdl for fit:"
## [1] " calling mypredict_mdl for OOB:"
## model_id model_method
## 1 All.X.bayesglm bayesglm
## feats
## 1 Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 1 1.709 0.112
## max.R.sq.fit min.RMSE.fit max.R.sq.OOB min.RMSE.OOB min.aic.fit
## 1 0.1976507 31.28241 NA NA 5372.264
## max.Rsquared.fit min.RMSESD.fit max.RsquaredSD.fit
## 1 0.07570071 1.446939 0.0266417
## label step_major step_minor bgn end elapsed
## 4 fit.models_1_bayesglm 4 0 39.446 42.138 2.692
## 5 fit.models_1_rpart 5 0 42.139 NA NA
## [1] "fitting model: All.X.no.rnorm.rpart"
## [1] " indep_vars: Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr"## Warning in nominalTrainWorkflow(x = x, y = y, wts = weights, info =
## trainInfo, : There were missing values in resampled performance measures.
## Aggregating results
## Selecting tuning parameters
## Fitting cp = 0.0349 on full training set
## Call:
## rpart(formula = .outcome ~ ., control = list(minsplit = 20, minbucket = 7,
## cp = 0, maxcompete = 4, maxsurrogate = 5, usesurrogate = 2,
## surrogatestyle = 0, maxdepth = 30, xval = 0))
## n= 556
##
## CP nsplit rel error
## 1 0.07579970 0 1.0000000
## 2 0.03490253 1 0.9242003
##
## Variable importance
## Worry.About.Info.my.fctr1 Tried.Masking.Identity.my.fctr1
## 76 9
## Privacy.Laws.Effective.my.fctr1 Region.fctrWest
## 5 4
## Age.my.fctr(33.6,49.2] Info.On.Internet.my.fctr5
## 4 2
##
## Node number 1: 556 observations, complexity param=0.0757997
## mean=62.54204, MSE=993.0631
## left son=2 (292 obs) right son=3 (264 obs)
## Primary splits:
## Worry.About.Info.my.fctr1 < 0.5 to the left, improve=0.075799700, (0 missing)
## Privacy.Laws.Effective.my.fctr1 < 0.5 to the right, improve=0.055656000, (0 missing)
## Age.my.fctr(33.6,49.2] < 0.5 to the left, improve=0.009163670, (0 missing)
## Tried.Masking.Identity.my.fctr1 < 0.5 to the left, improve=0.008489602, (0 missing)
## Info.On.Internet.my.fctr8 < 0.5 to the left, improve=0.007772879, (0 missing)
## Surrogate splits:
## Tried.Masking.Identity.my.fctr1 < 0.5 to the left, agree=0.579, adj=0.114, (0 split)
## Privacy.Laws.Effective.my.fctr1 < 0.5 to the right, agree=0.556, adj=0.064, (0 split)
## Region.fctrWest < 0.5 to the left, agree=0.552, adj=0.057, (0 split)
## Age.my.fctr(33.6,49.2] < 0.5 to the left, agree=0.549, adj=0.049, (0 split)
## Info.On.Internet.my.fctr5 < 0.5 to the left, agree=0.540, adj=0.030, (0 split)
##
## Node number 2: 292 observations
## mean=54.29244, MSE=1062.076
##
## Node number 3: 264 observations
## mean=71.66659, MSE=758.1997
##
## n= 556
##
## node), split, n, deviance, yval
## * denotes terminal node
##
## 1) root 556 552143.1 62.54204
## 2) Worry.About.Info.my.fctr1< 0.5 292 310126.1 54.29244 *
## 3) Worry.About.Info.my.fctr1>=0.5 264 200164.7 71.66659 *
## [1] " calling mypredict_mdl for fit:"
## [1] " calling mypredict_mdl for OOB:"
## model_id model_method
## 1 All.X.no.rnorm.rpart rpart
## feats
## 1 Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 3 1.071 0.065
## max.R.sq.fit min.RMSE.fit max.R.sq.OOB min.RMSE.OOB max.Rsquared.fit
## 1 0.0757997 30.69813 NA NA 0.05886582
## min.RMSESD.fit max.RsquaredSD.fit
## 1 0.8694026 0.03641824
## label step_major step_minor bgn end elapsed
## 5 fit.models_1_rpart 5 0 42.139 45.066 2.927
## 6 fit.models_1_rf 6 0 45.066 NA NA
## [1] "fitting model: All.X.no.rnorm.rf"
## [1] " indep_vars: Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr"## Loading required package: randomForest
## randomForest 4.6-10
## Type rfNews() to see new features/changes/bug fixes.
##
## Attaching package: 'randomForest'
##
## The following object is masked from 'package:dplyr':
##
## combine
## Aggregating results
## Selecting tuning parameters
## Fitting mtry = 2 on full training set## Warning in myfit_mdl(model_id = model_id, model_method = method,
## indep_vars_vctr = indep_vars_vctr, : model's bestTune found at an extreme
## of tuneGrid for parameter: mtry
## Length Class Mode
## call 4 -none- call
## type 1 -none- character
## predicted 556 -none- numeric
## mse 500 -none- numeric
## rsq 500 -none- numeric
## oob.times 556 -none- numeric
## importance 37 -none- numeric
## importanceSD 0 -none- NULL
## localImportance 0 -none- NULL
## proximity 0 -none- NULL
## ntree 1 -none- numeric
## mtry 1 -none- numeric
## forest 11 -none- list
## coefs 0 -none- NULL
## y 556 -none- numeric
## test 0 -none- NULL
## inbag 0 -none- NULL
## xNames 37 -none- character
## problemType 1 -none- character
## tuneValue 1 data.frame list
## obsLevels 1 -none- logical
## [1] " calling mypredict_mdl for fit:"
## [1] " calling mypredict_mdl for OOB:"
## model_id model_method
## 1 All.X.no.rnorm.rf rf
## feats
## 1 Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 3 7.635 0.627
## max.R.sq.fit min.RMSE.fit max.R.sq.OOB min.RMSE.OOB max.Rsquared.fit
## 1 0.2674834 30.40884 NA NA 0.08078154
## min.RMSESD.fit max.RsquaredSD.fit
## 1 0.667417 0.005363173# User specified
# easier to exclude features
#model_id_pfx <- "";
# indep_vars_vctr <- setdiff(names(glb_fitobs_df),
# union(union(glb_rsp_var, glb_exclude_vars_as_features),
# c("<feat1_name>", "<feat2_name>")))
# method <- ""
# easier to include features
# sav_models_lst <- glb_models_lst; sav_models_df <- glb_models_df; sav_featsimp_df <- glb_featsimp_df
# glb_models_lst <- sav_models_lst; glb_models_df <- sav_models_df; glm_featsimp_df <- sav_featsimp_df
#table(glb_allobs_df$myCategory, glb_allobs_df$H.P.readers.respond, glb_allobs_df[, glb_rsp_var], useNA="ifany")
#model_id <- "Rank9.2"; indep_vars_vctr <- c(NULL
# ,"<feat1>"
# ,"<feat1>*<feat2>"
# ,"<feat1>:<feat2>"
# )
# for (method in c("bayesglm")) {
# ret_lst <- myfit_mdl(model_id=model_id, model_method=method,
# indep_vars_vctr=indep_vars_vctr,
# model_type=glb_model_type,
# rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
# fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
# n_cv_folds=glb_n_cv_folds, tune_models_df=glb_tune_models_df)
# # csm_mdl_id <- paste0(model_id, ".", method)
# # csm_featsimp_df <- myget_feats_importance(glb_models_lst[[paste0(model_id, ".", method)]]); print(head(csm_featsimp_df))
# }
#csm_featsimp_df[grepl("H.npnct19.log", row.names(csm_featsimp_df)), , FALSE]
#csm_OOBobs_df <- glb_get_predictions(glb_OOBobs_df, mdl_id=csm_mdl_id, rsp_var_out=glb_rsp_var_out, prob_threshold_def=glb_models_df[glb_models_df$model_id == csm_mdl_id, "opt.prob.threshold.OOB"])
#print(sprintf("%s OOB confusion matrix & accuracy: ", csm_mdl_id)); print(t(confusionMatrix(csm_OOBobs_df[, paste0(glb_rsp_var_out, csm_mdl_id)], csm_OOBobs_df[, glb_rsp_var])$table))
#glb_models_df[, "max.Accuracy.OOB", FALSE]
#varImp(glb_models_lst[["Low.cor.X.glm"]])
#orderBy(~ -Overall, varImp(glb_models_lst[["All.X.2.glm"]])$importance)
#orderBy(~ -Overall, varImp(glb_models_lst[["All.X.3.glm"]])$importance)
#glb_feats_df[grepl("npnct28", glb_feats_df$id), ]
#print(sprintf("%s OOB confusion matrix & accuracy: ", glb_sel_mdl_id)); print(t(confusionMatrix(glb_OOBobs_df[, paste0(glb_rsp_var_out, glb_sel_mdl_id)], glb_OOBobs_df[, glb_rsp_var])$table))
# User specified bivariate models
# indep_vars_vctr_lst <- list()
# for (feat in setdiff(names(glb_fitobs_df),
# union(glb_rsp_var, glb_exclude_vars_as_features)))
# indep_vars_vctr_lst[["feat"]] <- feat
# User specified combinatorial models
# indep_vars_vctr_lst <- list()
# combn_mtrx <- combn(c("<feat1_name>", "<feat2_name>", "<featn_name>"),
# <num_feats_to_choose>)
# for (combn_ix in 1:ncol(combn_mtrx))
# #print(combn_mtrx[, combn_ix])
# indep_vars_vctr_lst[[combn_ix]] <- combn_mtrx[, combn_ix]
# template for myfit_mdl
# rf is hard-coded in caret to recognize only Accuracy / Kappa evaluation metrics
# only for OOB in trainControl ?
# ret_lst <- myfit_mdl_fn(model_id=paste0(model_id_pfx, ""), model_method=method,
# indep_vars_vctr=indep_vars_vctr,
# rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
# fit_df=glb_fitobs_df, OOB_df=glb_OOBobs_df,
# n_cv_folds=glb_n_cv_folds, tune_models_df=glb_tune_models_df,
# model_loss_mtrx=glb_model_metric_terms,
# model_summaryFunction=glb_model_metric_smmry,
# model_metric=glb_model_metric,
# model_metric_maximize=glb_model_metric_maximize)
# Simplify a model
# fit_df <- glb_fitobs_df; glb_mdl <- step(<complex>_mdl)
# Non-caret models
# rpart_area_mdl <- rpart(reformulate("Area", response=glb_rsp_var),
# data=glb_fitobs_df, #method="class",
# control=rpart.control(cp=0.12),
# parms=list(loss=glb_model_metric_terms))
# print("rpart_sel_wlm_mdl"); prp(rpart_sel_wlm_mdl)
#
print(glb_models_df)## model_id model_method
## MFO.lm MFO.lm lm
## Max.cor.Y.cv.0.rpart Max.cor.Y.cv.0.rpart rpart
## Max.cor.Y.cv.0.cp.0.rpart Max.cor.Y.cv.0.cp.0.rpart rpart
## Max.cor.Y.rpart Max.cor.Y.rpart rpart
## Max.cor.Y.lm Max.cor.Y.lm lm
## Low.cor.X.lm Low.cor.X.lm lm
## All.X.lm All.X.lm lm
## All.X.glm All.X.glm glm
## All.X.bayesglm All.X.bayesglm bayesglm
## All.X.no.rnorm.rpart All.X.no.rnorm.rpart rpart
## All.X.no.rnorm.rf All.X.no.rnorm.rf rf
## feats
## MFO.lm .rnorm
## Max.cor.Y.cv.0.rpart Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr
## Max.cor.Y.cv.0.cp.0.rpart Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr
## Max.cor.Y.rpart Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr
## Max.cor.Y.lm Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr
## Low.cor.X.lm Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## All.X.lm Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## All.X.glm Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## All.X.bayesglm Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## All.X.no.rnorm.rpart Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## All.X.no.rnorm.rf Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## max.nTuningRuns min.elapsedtime.everything
## MFO.lm 0 0.442
## Max.cor.Y.cv.0.rpart 0 0.532
## Max.cor.Y.cv.0.cp.0.rpart 0 0.466
## Max.cor.Y.rpart 3 0.947
## Max.cor.Y.lm 1 0.841
## Low.cor.X.lm 1 0.983
## All.X.lm 1 0.906
## All.X.glm 1 0.977
## All.X.bayesglm 1 1.709
## All.X.no.rnorm.rpart 3 1.071
## All.X.no.rnorm.rf 3 7.635
## min.elapsedtime.final max.R.sq.fit min.RMSE.fit
## MFO.lm 0.002 1.346478e-05 31.51269
## Max.cor.Y.cv.0.rpart 0.016 0.000000e+00 31.51290
## Max.cor.Y.cv.0.cp.0.rpart 0.015 1.228362e-01 29.51405
## Max.cor.Y.rpart 0.016 1.107022e-01 29.87947
## Max.cor.Y.lm 0.004 1.235906e-01 29.77477
## Low.cor.X.lm 0.015 1.976727e-01 31.31739
## All.X.lm 0.015 1.976727e-01 31.31739
## All.X.glm 0.067 1.976727e-01 31.31739
## All.X.bayesglm 0.112 1.976507e-01 31.28241
## All.X.no.rnorm.rpart 0.065 7.579970e-02 30.69813
## All.X.no.rnorm.rf 0.627 2.674834e-01 30.40884
## max.R.sq.OOB min.RMSE.OOB max.Adj.R.sq.fit
## MFO.lm NA NA -0.001791565
## Max.cor.Y.cv.0.rpart NA NA NA
## Max.cor.Y.cv.0.cp.0.rpart NA NA NA
## Max.cor.Y.rpart NA NA NA
## Max.cor.Y.lm NA NA 0.117228253
## Low.cor.X.lm NA NA 0.140363573
## All.X.lm NA NA 0.140363573
## All.X.glm NA NA NA
## All.X.bayesglm NA NA NA
## All.X.no.rnorm.rpart NA NA NA
## All.X.no.rnorm.rf NA NA NA
## max.Rsquared.fit min.RMSESD.fit
## MFO.lm NA NA
## Max.cor.Y.cv.0.rpart NA NA
## Max.cor.Y.cv.0.cp.0.rpart NA NA
## Max.cor.Y.rpart 0.10331231 0.8361541
## Max.cor.Y.lm 0.10892470 0.8402025
## Low.cor.X.lm 0.07528015 1.4694062
## All.X.lm 0.07528015 1.4694062
## All.X.glm 0.07528015 1.4694062
## All.X.bayesglm 0.07570071 1.4469388
## All.X.no.rnorm.rpart 0.05886582 0.8694026
## All.X.no.rnorm.rf 0.08078154 0.6674170
## max.RsquaredSD.fit min.aic.fit
## MFO.lm NA NA
## Max.cor.Y.cv.0.rpart NA NA
## Max.cor.Y.cv.0.cp.0.rpart NA NA
## Max.cor.Y.rpart 0.023796516 NA
## Max.cor.Y.lm 0.017588068 NA
## Low.cor.X.lm 0.026879886 NA
## All.X.lm 0.026879886 NA
## All.X.glm 0.026879886 5370.249
## All.X.bayesglm 0.026641704 5372.264
## All.X.no.rnorm.rpart 0.036418243 NA
## All.X.no.rnorm.rf 0.005363173 NArm(ret_lst)
fit.models_1_chunk_df <- myadd_chunk(fit.models_1_chunk_df, "fit.models_1_end",
major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 6 fit.models_1_rf 6 0 45.066 55.002 9.936
## 7 fit.models_1_end 7 0 55.002 NA NAglb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 11 fit.models 7 1 32.710 55.008 22.298
## 12 fit.models 7 2 55.008 NA NAif (!is.null(glb_model_metric_smmry)) {
stats_df <- glb_models_df[, "model_id", FALSE]
stats_mdl_df <- data.frame()
for (model_id in stats_df$model_id) {
stats_mdl_df <- rbind(stats_mdl_df,
mypredict_mdl(glb_models_lst[[model_id]], glb_fitobs_df, glb_rsp_var,
glb_rsp_var_out, model_id, "fit",
glb_model_metric_smmry, glb_model_metric,
glb_model_metric_maximize, ret_type="stats"))
}
stats_df <- merge(stats_df, stats_mdl_df, all.x=TRUE)
stats_mdl_df <- data.frame()
for (model_id in stats_df$model_id) {
stats_mdl_df <- rbind(stats_mdl_df,
mypredict_mdl(glb_models_lst[[model_id]], glb_OOBobs_df, glb_rsp_var,
glb_rsp_var_out, model_id, "OOB",
glb_model_metric_smmry, glb_model_metric,
glb_model_metric_maximize, ret_type="stats"))
}
stats_df <- merge(stats_df, stats_mdl_df, all.x=TRUE)
# tmp_models_df <- orderBy(~model_id, glb_models_df)
# rownames(tmp_models_df) <- seq(1, nrow(tmp_models_df))
# all.equal(subset(tmp_models_df[, names(stats_df)], model_id != "Random.myrandom_classfr"),
# subset(stats_df, model_id != "Random.myrandom_classfr"))
# print(subset(tmp_models_df[, names(stats_df)], model_id != "Random.myrandom_classfr")[, c("model_id", "max.Accuracy.fit")])
# print(subset(stats_df, model_id != "Random.myrandom_classfr")[, c("model_id", "max.Accuracy.fit")])
print("Merging following data into glb_models_df:")
print(stats_mrg_df <- stats_df[, c(1, grep(glb_model_metric, names(stats_df)))])
print(tmp_models_df <- orderBy(~model_id, glb_models_df[, c("model_id", grep(glb_model_metric, names(stats_df), value=TRUE))]))
tmp2_models_df <- glb_models_df[, c("model_id", setdiff(names(glb_models_df), grep(glb_model_metric, names(stats_df), value=TRUE)))]
tmp3_models_df <- merge(tmp2_models_df, stats_mrg_df, all.x=TRUE, sort=FALSE)
print(tmp3_models_df)
print(names(tmp3_models_df))
print(glb_models_df <- subset(tmp3_models_df, select=-model_id.1))
}
plt_models_df <- glb_models_df[, -grep("SD|Upper|Lower", names(glb_models_df))]
for (var in grep("^min.", names(plt_models_df), value=TRUE)) {
plt_models_df[, sub("min.", "inv.", var)] <-
#ifelse(all(is.na(tmp <- plt_models_df[, var])), NA, 1.0 / tmp)
1.0 / plt_models_df[, var]
plt_models_df <- plt_models_df[ , -grep(var, names(plt_models_df))]
}
print(plt_models_df)## model_id model_method
## MFO.lm MFO.lm lm
## Max.cor.Y.cv.0.rpart Max.cor.Y.cv.0.rpart rpart
## Max.cor.Y.cv.0.cp.0.rpart Max.cor.Y.cv.0.cp.0.rpart rpart
## Max.cor.Y.rpart Max.cor.Y.rpart rpart
## Max.cor.Y.lm Max.cor.Y.lm lm
## Low.cor.X.lm Low.cor.X.lm lm
## All.X.lm All.X.lm lm
## All.X.glm All.X.glm glm
## All.X.bayesglm All.X.bayesglm bayesglm
## All.X.no.rnorm.rpart All.X.no.rnorm.rpart rpart
## All.X.no.rnorm.rf All.X.no.rnorm.rf rf
## feats
## MFO.lm .rnorm
## Max.cor.Y.cv.0.rpart Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr
## Max.cor.Y.cv.0.cp.0.rpart Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr
## Max.cor.Y.rpart Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr
## Max.cor.Y.lm Worry.About.Info.my.fctr, Privacy.Laws.Effective.my.fctr
## Low.cor.X.lm Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## All.X.lm Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## All.X.glm Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## All.X.bayesglm Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## All.X.no.rnorm.rpart Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## All.X.no.rnorm.rf Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## max.nTuningRuns max.R.sq.fit max.R.sq.OOB
## MFO.lm 0 1.346478e-05 NA
## Max.cor.Y.cv.0.rpart 0 0.000000e+00 NA
## Max.cor.Y.cv.0.cp.0.rpart 0 1.228362e-01 NA
## Max.cor.Y.rpart 3 1.107022e-01 NA
## Max.cor.Y.lm 1 1.235906e-01 NA
## Low.cor.X.lm 1 1.976727e-01 NA
## All.X.lm 1 1.976727e-01 NA
## All.X.glm 1 1.976727e-01 NA
## All.X.bayesglm 1 1.976507e-01 NA
## All.X.no.rnorm.rpart 3 7.579970e-02 NA
## All.X.no.rnorm.rf 3 2.674834e-01 NA
## max.Adj.R.sq.fit max.Rsquared.fit
## MFO.lm -0.001791565 NA
## Max.cor.Y.cv.0.rpart NA NA
## Max.cor.Y.cv.0.cp.0.rpart NA NA
## Max.cor.Y.rpart NA 0.10331231
## Max.cor.Y.lm 0.117228253 0.10892470
## Low.cor.X.lm 0.140363573 0.07528015
## All.X.lm 0.140363573 0.07528015
## All.X.glm NA 0.07528015
## All.X.bayesglm NA 0.07570071
## All.X.no.rnorm.rpart NA 0.05886582
## All.X.no.rnorm.rf NA 0.08078154
## inv.elapsedtime.everything inv.elapsedtime.final
## MFO.lm 2.2624434 500.000000
## Max.cor.Y.cv.0.rpart 1.8796992 62.500000
## Max.cor.Y.cv.0.cp.0.rpart 2.1459227 66.666667
## Max.cor.Y.rpart 1.0559662 62.500000
## Max.cor.Y.lm 1.1890606 250.000000
## Low.cor.X.lm 1.0172940 66.666667
## All.X.lm 1.1037528 66.666667
## All.X.glm 1.0235415 14.925373
## All.X.bayesglm 0.5851375 8.928571
## All.X.no.rnorm.rpart 0.9337068 15.384615
## All.X.no.rnorm.rf 0.1309758 1.594896
## inv.RMSE.fit inv.RMSE.OOB inv.aic.fit
## MFO.lm 0.03173325 NA NA
## Max.cor.Y.cv.0.rpart 0.03173303 NA NA
## Max.cor.Y.cv.0.cp.0.rpart 0.03388217 NA NA
## Max.cor.Y.rpart 0.03346779 NA NA
## Max.cor.Y.lm 0.03358548 NA NA
## Low.cor.X.lm 0.03193114 NA NA
## All.X.lm 0.03193114 NA NA
## All.X.glm 0.03193114 NA 0.0001862111
## All.X.bayesglm 0.03196684 NA 0.0001861413
## All.X.no.rnorm.rpart 0.03257527 NA NA
## All.X.no.rnorm.rf 0.03288518 NA NAprint(myplot_radar(radar_inp_df=plt_models_df))## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 11. Consider specifying shapes manually. if you must have them.## Warning in loop_apply(n, do.ply): Removed 7 rows containing missing values
## (geom_path).## Warning in loop_apply(n, do.ply): Removed 48 rows containing missing values
## (geom_point).## Warning in loop_apply(n, do.ply): Removed 19 rows containing missing values
## (geom_text).## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 11. Consider specifying shapes manually. if you must have them.
# print(myplot_radar(radar_inp_df=subset(plt_models_df,
# !(model_id %in% grep("random|MFO", plt_models_df$model_id, value=TRUE)))))
# Compute CI for <metric>SD
glb_models_df <- mutate(glb_models_df,
max.df = ifelse(max.nTuningRuns > 1, max.nTuningRuns - 1, NA),
min.sd2ci.scaler = ifelse(is.na(max.df), NA, qt(0.975, max.df)))
for (var in grep("SD", names(glb_models_df), value=TRUE)) {
# Does CI alredy exist ?
var_components <- unlist(strsplit(var, "SD"))
varActul <- paste0(var_components[1], var_components[2])
varUpper <- paste0(var_components[1], "Upper", var_components[2])
varLower <- paste0(var_components[1], "Lower", var_components[2])
if (varUpper %in% names(glb_models_df)) {
warning(varUpper, " already exists in glb_models_df")
# Assuming Lower also exists
next
}
print(sprintf("var:%s", var))
# CI is dependent on sample size in t distribution; df=n-1
glb_models_df[, varUpper] <- glb_models_df[, varActul] +
glb_models_df[, "min.sd2ci.scaler"] * glb_models_df[, var]
glb_models_df[, varLower] <- glb_models_df[, varActul] -
glb_models_df[, "min.sd2ci.scaler"] * glb_models_df[, var]
}## [1] "var:min.RMSESD.fit"
## [1] "var:max.RsquaredSD.fit"# Plot metrics with CI
plt_models_df <- glb_models_df[, "model_id", FALSE]
pltCI_models_df <- glb_models_df[, "model_id", FALSE]
for (var in grep("Upper", names(glb_models_df), value=TRUE)) {
var_components <- unlist(strsplit(var, "Upper"))
col_name <- unlist(paste(var_components, collapse=""))
plt_models_df[, col_name] <- glb_models_df[, col_name]
for (name in paste0(var_components[1], c("Upper", "Lower"), var_components[2]))
pltCI_models_df[, name] <- glb_models_df[, name]
}
build_statsCI_data <- function(plt_models_df) {
mltd_models_df <- melt(plt_models_df, id.vars="model_id")
mltd_models_df$data <- sapply(1:nrow(mltd_models_df),
function(row_ix) tail(unlist(strsplit(as.character(
mltd_models_df[row_ix, "variable"]), "[.]")), 1))
mltd_models_df$label <- sapply(1:nrow(mltd_models_df),
function(row_ix) head(unlist(strsplit(as.character(
mltd_models_df[row_ix, "variable"]),
paste0(".", mltd_models_df[row_ix, "data"]))), 1))
#print(mltd_models_df)
return(mltd_models_df)
}
mltd_models_df <- build_statsCI_data(plt_models_df)
mltdCI_models_df <- melt(pltCI_models_df, id.vars="model_id")
for (row_ix in 1:nrow(mltdCI_models_df)) {
for (type in c("Upper", "Lower")) {
if (length(var_components <- unlist(strsplit(
as.character(mltdCI_models_df[row_ix, "variable"]), type))) > 1) {
#print(sprintf("row_ix:%d; type:%s; ", row_ix, type))
mltdCI_models_df[row_ix, "label"] <- var_components[1]
mltdCI_models_df[row_ix, "data"] <-
unlist(strsplit(var_components[2], "[.]"))[2]
mltdCI_models_df[row_ix, "type"] <- type
break
}
}
}
#print(mltdCI_models_df)
# castCI_models_df <- dcast(mltdCI_models_df, value ~ type, fun.aggregate=sum)
# print(castCI_models_df)
wideCI_models_df <- reshape(subset(mltdCI_models_df, select=-variable),
timevar="type",
idvar=setdiff(names(mltdCI_models_df), c("type", "value", "variable")),
direction="wide")
#print(wideCI_models_df)
mrgdCI_models_df <- merge(wideCI_models_df, mltd_models_df, all.x=TRUE)
#print(mrgdCI_models_df)
# Merge stats back in if CIs don't exist
goback_vars <- c()
for (var in unique(mltd_models_df$label)) {
for (type in unique(mltd_models_df$data)) {
var_type <- paste0(var, ".", type)
# if this data is already present, next
if (var_type %in% unique(paste(mltd_models_df$label, mltd_models_df$data,
sep=".")))
next
#print(sprintf("var_type:%s", var_type))
goback_vars <- c(goback_vars, var_type)
}
}
if (length(goback_vars) > 0) {
mltd_goback_df <- build_statsCI_data(glb_models_df[, c("model_id", goback_vars)])
mltd_models_df <- rbind(mltd_models_df, mltd_goback_df)
}
mltd_models_df <- merge(mltd_models_df, glb_models_df[, c("model_id", "model_method")],
all.x=TRUE)
png(paste0(glb_out_pfx, "models_bar.png"), width=480*3, height=480*2)
print(gp <- myplot_bar(mltd_models_df, "model_id", "value", colorcol_name="model_method") +
geom_errorbar(data=mrgdCI_models_df,
mapping=aes(x=model_id, ymax=value.Upper, ymin=value.Lower), width=0.5) +
facet_grid(label ~ data, scales="free") +
theme(axis.text.x = element_text(angle = 90,vjust = 0.5)))## Warning in loop_apply(n, do.ply): Removed 3 rows containing missing values
## (position_stack).dev.off()## quartz_off_screen
## 2print(gp)## Warning in loop_apply(n, do.ply): Removed 3 rows containing missing values
## (position_stack).
# used for console inspection
model_evl_terms <- c(NULL)
for (metric in glb_model_evl_criteria)
model_evl_terms <- c(model_evl_terms,
ifelse(length(grep("max", metric)) > 0, "-", "+"), metric)
if (glb_is_classification && glb_is_binomial)
model_evl_terms <- c(model_evl_terms, "-", "opt.prob.threshold.OOB")
model_sel_frmla <- as.formula(paste(c("~ ", model_evl_terms), collapse=" "))
dsp_models_cols <- c("model_id", glb_model_evl_criteria)
if (glb_is_classification && glb_is_binomial)
dsp_models_cols <- c(dsp_models_cols, "opt.prob.threshold.OOB")
print(dsp_models_df <- orderBy(model_sel_frmla, glb_models_df)[, dsp_models_cols])## model_id min.RMSE.OOB max.R.sq.OOB max.Adj.R.sq.fit
## 6 Low.cor.X.lm NA NA 0.140363573
## 7 All.X.lm NA NA 0.140363573
## 5 Max.cor.Y.lm NA NA 0.117228253
## 1 MFO.lm NA NA -0.001791565
## 2 Max.cor.Y.cv.0.rpart NA NA NA
## 3 Max.cor.Y.cv.0.cp.0.rpart NA NA NA
## 4 Max.cor.Y.rpart NA NA NA
## 8 All.X.glm NA NA NA
## 9 All.X.bayesglm NA NA NA
## 10 All.X.no.rnorm.rpart NA NA NA
## 11 All.X.no.rnorm.rf NA NA NAprint(myplot_radar(radar_inp_df=dsp_models_df))## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 11. Consider specifying shapes manually. if you must have them.## Warning in loop_apply(n, do.ply): Removed 11 rows containing missing values
## (geom_point).## Warning in loop_apply(n, do.ply): Removed 7 rows containing missing values
## (geom_text).## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set1 is 9
## Returning the palette you asked for with that many colors## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have
## 11. Consider specifying shapes manually. if you must have them.
print("Metrics used for model selection:"); print(model_sel_frmla)## [1] "Metrics used for model selection:"## ~+min.RMSE.OOB - max.R.sq.OOB - max.Adj.R.sq.fitprint(sprintf("Best model id: %s", dsp_models_df[1, "model_id"]))## [1] "Best model id: Low.cor.X.lm"if (is.null(glb_sel_mdl_id)) {
glb_sel_mdl_id <- dsp_models_df[1, "model_id"]
if (glb_sel_mdl_id == "Interact.High.cor.Y.glm") {
warning("glb_sel_mdl_id: Interact.High.cor.Y.glm; myextract_mdl_feats does not currently support interaction terms")
glb_sel_mdl_id <- dsp_models_df[2, "model_id"]
}
} else
print(sprintf("User specified selection: %s", glb_sel_mdl_id))
myprint_mdl(glb_sel_mdl <- glb_models_lst[[glb_sel_mdl_id]])
## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced
##
## Call:
## lm(formula = .outcome ~ ., data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -76.048 -19.249 4.149 21.387 65.612
##
## Coefficients: (1 not defined because of singularities)
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 34.9170 12.4594 2.802 0.00526
## Worry.About.Info.my.fctr1 13.7799 2.6606 5.179 3.20e-07
## Worry.About.Info.my.fctrNA.my -57.2029 30.1759 -1.896 0.05856
## `Age.my.fctr(33.6,49.2]` 11.0518 3.7471 2.949 0.00333
## `Age.my.fctr(49.2,64.8]` 10.9517 3.4654 3.160 0.00167
## `Age.my.fctr(64.8,80.4]` 1.8203 4.3536 0.418 0.67604
## `Age.my.fctr(80.4,96.1]` 2.4955 9.2478 0.270 0.78738
## Age.my.fctrNA.my 14.7688 8.7521 1.687 0.09212
## Tried.Masking.Identity.my.fctr1 4.6212 3.5949 1.285 0.19920
## Tried.Masking.Identity.my.fctrNA.my -6.8003 13.4700 -0.505 0.61388
## Internet.Use.my 17.9850 9.8992 1.817 0.06982
## Sex.fctrFemale 2.2626 2.6248 0.862 0.38909
## Conservativeness.my.fctr2 0.8528 6.4467 0.132 0.89481
## Conservativeness.my.fctr3 5.3331 5.9749 0.893 0.37249
## Conservativeness.my.fctr4 4.5422 5.9929 0.758 0.44884
## Conservativeness.my.fctr5 3.9890 7.0603 0.565 0.57232
## Conservativeness.my.fctrNA.my 5.1013 7.9028 0.646 0.51888
## Smartphone.my.fctr1 2.6720 2.9600 0.903 0.36709
## Smartphone.my.fctrNA.my 0.6564 8.4128 0.078 0.93784
## .rnorm -0.1930 1.2831 -0.150 0.88049
## Info.On.Internet.my.fctr1 -0.7005 5.4397 -0.129 0.89759
## Info.On.Internet.my.fctr10 -20.7025 10.8093 -1.915 0.05601
## Info.On.Internet.my.fctr11 16.5327 13.7849 1.199 0.23095
## Info.On.Internet.my.fctr2 -10.2710 5.0344 -2.040 0.04184
## Info.On.Internet.my.fctr3 -7.8068 5.1808 -1.507 0.13245
## Info.On.Internet.my.fctr4 -8.5032 5.0476 -1.685 0.09267
## Info.On.Internet.my.fctr5 -6.3418 5.4519 -1.163 0.24527
## Info.On.Internet.my.fctr6 -7.9571 5.8301 -1.365 0.17290
## Info.On.Internet.my.fctr7 -9.1325 5.8907 -1.550 0.12167
## Info.On.Internet.my.fctr8 4.3286 6.6599 0.650 0.51602
## Info.On.Internet.my.fctr9 -7.5259 9.1857 -0.819 0.41299
## Info.On.Internet.my.fctrNA.my NA NA NA NA
## Region.fctrSouth 2.2245 4.0273 0.552 0.58094
## Region.fctrWest 0.1380 4.2571 0.032 0.97414
## Region.fctrMidwest -0.2835 4.3720 -0.065 0.94832
## Anonymity.Possible.my.fctr1 -3.8693 2.6915 -1.438 0.15115
## Anonymity.Possible.my.fctrNA.my 1.9033 6.1261 0.311 0.75617
## Privacy.Laws.Effective.my.fctr1 -14.8815 3.1009 -4.799 2.09e-06
## Privacy.Laws.Effective.my.fctrNA.my -6.7398 4.7663 -1.414 0.15795
##
## (Intercept) **
## Worry.About.Info.my.fctr1 ***
## Worry.About.Info.my.fctrNA.my .
## `Age.my.fctr(33.6,49.2]` **
## `Age.my.fctr(49.2,64.8]` **
## `Age.my.fctr(64.8,80.4]`
## `Age.my.fctr(80.4,96.1]`
## Age.my.fctrNA.my .
## Tried.Masking.Identity.my.fctr1
## Tried.Masking.Identity.my.fctrNA.my
## Internet.Use.my .
## Sex.fctrFemale
## Conservativeness.my.fctr2
## Conservativeness.my.fctr3
## Conservativeness.my.fctr4
## Conservativeness.my.fctr5
## Conservativeness.my.fctrNA.my
## Smartphone.my.fctr1
## Smartphone.my.fctrNA.my
## .rnorm
## Info.On.Internet.my.fctr1
## Info.On.Internet.my.fctr10 .
## Info.On.Internet.my.fctr11
## Info.On.Internet.my.fctr2 *
## Info.On.Internet.my.fctr3
## Info.On.Internet.my.fctr4 .
## Info.On.Internet.my.fctr5
## Info.On.Internet.my.fctr6
## Info.On.Internet.my.fctr7
## Info.On.Internet.my.fctr8
## Info.On.Internet.my.fctr9
## Info.On.Internet.my.fctrNA.my
## Region.fctrSouth
## Region.fctrWest
## Region.fctrMidwest
## Anonymity.Possible.my.fctr1
## Anonymity.Possible.my.fctrNA.my
## Privacy.Laws.Effective.my.fctr1 ***
## Privacy.Laws.Effective.my.fctrNA.my
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 29.24 on 518 degrees of freedom
## Multiple R-squared: 0.1977, Adjusted R-squared: 0.1404
## F-statistic: 3.449 on 37 and 518 DF, p-value: 2.31e-10## [1] TRUE# From here to save(), this should all be in one function
# these are executed in the same seq twice more:
# fit.data.training & predict.data.new chunks
glb_get_predictions <- function(df, mdl_id, rsp_var_out, prob_threshold_def=NULL) {
mdl <- glb_models_lst[[mdl_id]]
rsp_var_out <- paste0(rsp_var_out, mdl_id)
if (glb_is_regression) {
df[, rsp_var_out] <- predict(mdl, newdata=df, type="raw")
print(myplot_scatter(df, glb_rsp_var, rsp_var_out, smooth=TRUE))
df[, paste0(rsp_var_out, ".err")] <-
abs(df[, rsp_var_out] - df[, glb_rsp_var])
print(head(orderBy(reformulate(c("-", paste0(rsp_var_out, ".err"))),
df)))
}
if (glb_is_classification && glb_is_binomial) {
prob_threshold <- glb_models_df[glb_models_df$model_id == mdl_id,
"opt.prob.threshold.OOB"]
if (is.null(prob_threshold) || is.na(prob_threshold)) {
warning("Using default probability threshold: ", prob_threshold_def)
if (is.null(prob_threshold <- prob_threshold_def))
stop("Default probability threshold is NULL")
}
df[, paste0(rsp_var_out, ".prob")] <-
predict(mdl, newdata=df, type="prob")[, 2]
df[, rsp_var_out] <-
factor(levels(df[, glb_rsp_var])[
(df[, paste0(rsp_var_out, ".prob")] >=
prob_threshold) * 1 + 1], levels(df[, glb_rsp_var]))
# prediction stats already reported by myfit_mdl ???
}
if (glb_is_classification && !glb_is_binomial) {
df[, rsp_var_out] <- predict(mdl, newdata=df, type="raw")
df[, paste0(rsp_var_out, ".prob")] <-
predict(mdl, newdata=df, type="prob")
}
return(df)
}
glb_OOBobs_df <- glb_get_predictions(df=glb_OOBobs_df, mdl_id=glb_sel_mdl_id,
rsp_var_out=glb_rsp_var_out)## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Internet.Use Smartphone Sex Age State Region
## 794 1 1 Female 49 Virginia South
## 80 1 0 Male 21 Florida South
## 683 1 1 Male 43 North Carolina South
## 460 1 0 Female 62 Virginia South
## 954 1 1 Female 62 Florida South
## 632 1 0 Female 55 Alabama South
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 794 3 0 1 11.11111
## 80 3 8 1 0.00000
## 683 3 0 0 0.00000
## 460 2 8 1 0.00000
## 954 4 3 0 0.00000
## 632 2 0 0 0.00000
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 794 1 0 0
## 80 1 0 0
## 683 0 0 0
## 460 0 0 1
## 954 NA 0 0
## 632 0 0 0
## .rownames .src .rnorm Internet.Use.my Age.my.fctr
## 794 794 Test -0.3440475 1 (33.6,49.2]
## 80 80 Test 0.5643370 1 (17.9,33.6]
## 683 683 Test -0.3761202 1 (33.6,49.2]
## 460 460 Test -1.1358528 1 (49.2,64.8]
## 954 954 Test 0.3327613 1 (49.2,64.8]
## 632 632 Test -0.6707990 1 (49.2,64.8]
## Anonymity.Possible.my.fctr Conservativeness.my.fctr
## 794 1 3
## 80 1 3
## 683 0 3
## 460 0 2
## 954 NA.my 4
## 632 0 2
## Info.On.Internet.my.fctr Privacy.Laws.Effective.my.fctr
## 794 0 0
## 80 8 0
## 683 0 0
## 460 8 1
## 954 3 0
## 632 0 0
## Smartphone.my.fctr Tried.Masking.Identity.my.fctr
## 794 1 0
## 80 0 0
## 683 1 0
## 460 0 0
## 954 1 0
## 632 0 0
## Worry.About.Info.my.fctr Sex.fctr State.fctr Region.fctr
## 794 1 Female Virginia South
## 80 1 Male Florida South
## 683 0 Male North Carolina South
## 460 1 Female Virginia South
## 954 0 Female Florida South
## 632 0 Female Alabama South
## Privacy.Importance.predict.Low.cor.X.lm
## 794 86.42286
## 80 74.58973
## 683 74.25595
## 460 72.63961
## 954 69.58716
## 632 69.32296
## Privacy.Importance.predict.Low.cor.X.lm.err
## 794 75.31175
## 80 74.58973
## 683 74.25595
## 460 72.63961
## 954 69.58716
## 632 69.32296predct_accurate_var_name <- paste0(glb_rsp_var_out, glb_sel_mdl_id, ".accurate")
glb_OOBobs_df[, predct_accurate_var_name] <-
(glb_OOBobs_df[, glb_rsp_var] ==
glb_OOBobs_df[, paste0(glb_rsp_var_out, glb_sel_mdl_id)])
#stop(here"); sav_models_lst <- glb_models_lst; sav_models_df <- glb_models_df
glb_featsimp_df <-
myget_feats_importance(mdl=glb_sel_mdl, featsimp_df=NULL)
glb_featsimp_df[, paste0(glb_sel_mdl_id, ".importance")] <- glb_featsimp_df$importance
print(glb_featsimp_df)## importance Low.cor.X.lm.importance
## Worry.About.Info.my.fctr1 100.0000000 100.0000000
## Privacy.Laws.Effective.my.fctr1 92.6128304 92.6128304
## `Age.my.fctr(49.2,64.8]` 60.7732556 60.7732556
## `Age.my.fctr(33.6,49.2]` 56.6756161 56.6756161
## Info.On.Internet.my.fctr2 39.0097635 39.0097635
## Info.On.Internet.my.fctr10 36.5824483 36.5824483
## Worry.About.Info.my.fctrNA.my 36.2015544 36.2015544
## Internet.Use.my 34.6695694 34.6695694
## Age.my.fctrNA.my 32.1563634 32.1563634
## Info.On.Internet.my.fctr4 32.1007392 32.1007392
## Info.On.Internet.my.fctr7 29.4920157 29.4920157
## Info.On.Internet.my.fctr3 28.6475914 28.6475914
## Anonymity.Possible.my.fctr1 27.3021584 27.3021584
## Privacy.Laws.Effective.my.fctrNA.my 26.8441377 26.8441377
## Info.On.Internet.my.fctr6 25.8877833 25.8877833
## Tried.Masking.Identity.my.fctr1 24.3459375 24.3459375
## Info.On.Internet.my.fctr11 22.6724300 22.6724300
## Info.On.Internet.my.fctr5 21.9709901 21.9709901
## Smartphone.my.fctr1 16.9094201 16.9094201
## Conservativeness.my.fctr3 16.7124321 16.7124321
## Sex.fctrFemale 16.1181262 16.1181262
## Info.On.Internet.my.fctr9 15.2886330 15.2886330
## Conservativeness.my.fctr4 14.0961369 14.0961369
## Info.On.Internet.my.fctr8 11.9980054 11.9980054
## Conservativeness.my.fctrNA.my 11.9118764 11.9118764
## Conservativeness.my.fctr5 10.3474601 10.3474601
## Region.fctrSouth 10.1019949 10.1019949
## Tried.Masking.Identity.my.fctrNA.my 9.1788768 9.1788768
## `Age.my.fctr(64.8,80.4]` 7.4936724 7.4936724
## Anonymity.Possible.my.fctrNA.my 5.4063607 5.4063607
## `Age.my.fctr(80.4,96.1]` 4.6130643 4.6130643
## .rnorm 2.2924783 2.2924783
## Conservativeness.my.fctr2 1.9402339 1.9402339
## Info.On.Internet.my.fctr1 1.8719519 1.8719519
## Smartphone.my.fctrNA.my 0.8859963 0.8859963
## Region.fctrMidwest 0.6299939 0.6299939
## Region.fctrWest 0.0000000 0.0000000# Used again in fit.data.training & predict.data.new chunks
glb_analytics_diag_plots <- function(obs_df, mdl_id, prob_threshold=NULL) {
featsimp_df <- glb_featsimp_df
featsimp_df$feat <- gsub("`(.*?)`", "\\1", row.names(featsimp_df))
featsimp_df$feat.interact <- gsub("(.*?):(.*)", "\\2", featsimp_df$feat)
featsimp_df$feat <- gsub("(.*?):(.*)", "\\1", featsimp_df$feat)
featsimp_df$feat.interact <- ifelse(featsimp_df$feat.interact == featsimp_df$feat,
NA, featsimp_df$feat.interact)
featsimp_df$feat <- gsub("(.*?)\\.fctr(.*)", "\\1\\.fctr", featsimp_df$feat)
featsimp_df$feat.interact <- gsub("(.*?)\\.fctr(.*)", "\\1\\.fctr", featsimp_df$feat.interact)
featsimp_df <- orderBy(~ -importance.max, summaryBy(importance ~ feat + feat.interact,
data=featsimp_df, FUN=max))
#rex_str=":(.*)"; txt_vctr=tail(featsimp_df$feat); ret_lst <- regexec(rex_str, txt_vctr); ret_lst <- regmatches(txt_vctr, ret_lst); ret_vctr <- sapply(1:length(ret_lst), function(pos_ix) ifelse(length(ret_lst[[pos_ix]]) > 0, ret_lst[[pos_ix]], "")); print(ret_vctr <- ret_vctr[ret_vctr != ""])
if (nrow(featsimp_df) > 5) {
warning("Limiting important feature scatter plots to 5 out of ", nrow(featsimp_df))
featsimp_df <- head(featsimp_df, 5)
}
# if (!all(is.na(featsimp_df$feat.interact)))
# stop("not implemented yet")
rsp_var_out <- paste0(glb_rsp_var_out, mdl_id)
for (var in featsimp_df$feat) {
plot_df <- melt(obs_df, id.vars=var,
measure.vars=c(glb_rsp_var, rsp_var_out))
# if (var == "<feat_name>") print(myplot_scatter(plot_df, var, "value",
# facet_colcol_name="variable") +
# geom_vline(xintercept=<divider_val>, linetype="dotted")) else
print(myplot_scatter(plot_df, var, "value", colorcol_name="variable",
facet_colcol_name="variable", jitter=TRUE) +
guides(color=FALSE))
}
if (glb_is_regression) {
if (nrow(featsimp_df) == 0)
warning("No important features in glb_fin_mdl") else
print(myplot_prediction_regression(df=obs_df,
feat_x=ifelse(nrow(featsimp_df) > 1, featsimp_df$feat[2],
".rownames"),
feat_y=featsimp_df$feat[1],
rsp_var=glb_rsp_var, rsp_var_out=rsp_var_out,
id_vars=glb_id_var)
# + facet_wrap(reformulate(featsimp_df$feat[2])) # if [1 or 2] is a factor
# + geom_point(aes_string(color="<col_name>.fctr")) # to color the plot
)
}
if (glb_is_classification) {
if (nrow(featsimp_df) == 0)
warning("No features in selected model are statistically important")
else print(myplot_prediction_classification(df=obs_df,
feat_x=ifelse(nrow(featsimp_df) > 1, featsimp_df$feat[2],
".rownames"),
feat_y=featsimp_df$feat[1],
rsp_var=glb_rsp_var,
rsp_var_out=rsp_var_out,
id_vars=glb_id_var,
prob_threshold=prob_threshold)
# + geom_hline(yintercept=<divider_val>, linetype = "dotted")
)
}
}
if (glb_is_classification && glb_is_binomial)
glb_analytics_diag_plots(obs_df=glb_OOBobs_df, mdl_id=glb_sel_mdl_id,
prob_threshold=glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"opt.prob.threshold.OOB"]) else
glb_analytics_diag_plots(obs_df=glb_OOBobs_df, mdl_id=glb_sel_mdl_id) ## Warning in glb_analytics_diag_plots(obs_df = glb_OOBobs_df, mdl_id =
## glb_sel_mdl_id): Limiting important feature scatter plots to 5 out of 12## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Internet.Use Smartphone Sex Age State Region
## 794 1 1 Female 49 Virginia South
## 80 1 0 Male 21 Florida South
## 683 1 1 Male 43 North Carolina South
## 460 1 0 Female 62 Virginia South
## 954 1 1 Female 62 Florida South
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 794 3 0 1 11.11111
## 80 3 8 1 0.00000
## 683 3 0 0 0.00000
## 460 2 8 1 0.00000
## 954 4 3 0 0.00000
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 794 1 0 0
## 80 1 0 0
## 683 0 0 0
## 460 0 0 1
## 954 NA 0 0
## .rownames .src .rnorm Internet.Use.my Age.my.fctr
## 794 794 Test -0.3440475 1 (33.6,49.2]
## 80 80 Test 0.5643370 1 (17.9,33.6]
## 683 683 Test -0.3761202 1 (33.6,49.2]
## 460 460 Test -1.1358528 1 (49.2,64.8]
## 954 954 Test 0.3327613 1 (49.2,64.8]
## Anonymity.Possible.my.fctr Conservativeness.my.fctr
## 794 1 3
## 80 1 3
## 683 0 3
## 460 0 2
## 954 NA.my 4
## Info.On.Internet.my.fctr Privacy.Laws.Effective.my.fctr
## 794 0 0
## 80 8 0
## 683 0 0
## 460 8 1
## 954 3 0
## Smartphone.my.fctr Tried.Masking.Identity.my.fctr
## 794 1 0
## 80 0 0
## 683 1 0
## 460 0 0
## 954 1 0
## Worry.About.Info.my.fctr Sex.fctr State.fctr Region.fctr
## 794 1 Female Virginia South
## 80 1 Male Florida South
## 683 0 Male North Carolina South
## 460 1 Female Virginia South
## 954 0 Female Florida South
## Privacy.Importance.predict.Low.cor.X.lm
## 794 86.42286
## 80 74.58973
## 683 74.25595
## 460 72.63961
## 954 69.58716
## Privacy.Importance.predict.Low.cor.X.lm.err
## 794 75.31175
## 80 74.58973
## 683 74.25595
## 460 72.63961
## 954 69.58716
## Privacy.Importance.predict.Low.cor.X.lm.accurate .label
## 794 FALSE 794
## 80 FALSE 80
## 683 FALSE 683
## 460 FALSE 460
## 954 FALSE 954## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
# gather predictions from models better than MFO.*
#mdl_id <- "Conditional.X.rf"
#mdl_id <- "Conditional.X.cp.0.rpart"
#mdl_id <- "Conditional.X.rpart"
# glb_OOBobs_df <- glb_get_predictions(df=glb_OOBobs_df, mdl_id,
# glb_rsp_var_out)
# print(t(confusionMatrix(glb_OOBobs_df[, paste0(glb_rsp_var_out, mdl_id)],
# glb_OOBobs_df[, glb_rsp_var])$table))
FN_OOB_ids <- c(4721, 4020, 693, 92)
print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])## [1] Privacy.Importance
## [2] Privacy.Importance.predict.Low.cor.X.lm
## [3] Privacy.Importance.predict.Low.cor.X.lm.err
## [4] Privacy.Importance.predict.Low.cor.X.lm.accurate
## <0 rows> (or 0-length row.names)print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
glb_feats_df$id[1:5]])## [1] Worry.About.Info Worry.About.Info.my.fctr
## [3] Tried.Masking.Identity Age.my.fctr
## [5] Tried.Masking.Identity.my.fctr
## <0 rows> (or 0-length row.names)print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
glb_txt_vars])## data frame with 0 columns and 0 rowswrite.csv(glb_OOBobs_df[, c(glb_id_var,
grep(glb_rsp_var, names(glb_OOBobs_df), fixed=TRUE, value=TRUE))],
paste0(gsub(".", "_", paste0(glb_out_pfx, glb_sel_mdl_id), fixed=TRUE),
"_OOBobs.csv"), row.names=FALSE)
# print(glb_allobs_df[glb_allobs_df$UniqueID %in% FN_OOB_ids,
# glb_txt_vars])
# dsp_tbl(Headline.contains="[Ee]bola")
# sum(sel_obs(Headline.contains="[Ee]bola"))
# ftable(xtabs(Popular ~ NewsDesk.fctr, data=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,]))
# xtabs(NewsDesk ~ Popular, #Popular ~ NewsDesk.fctr,
# data=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,],
# exclude=NULL)
# print(mycreate_xtab_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,], c("Popular", "NewsDesk", "SectionName", "SubsectionName")))
# print(mycreate_tbl_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,], c("Popular", "NewsDesk", "SectionName", "SubsectionName")))
# print(mycreate_tbl_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,], c("Popular")))
# print(mycreate_tbl_df(df=glb_allobs_df[sel_obs(Headline.contains="[Ee]bola") ,],
# tbl_col_names=c("Popular", "NewsDesk")))
glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.models", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 12 fit.models 7 2 55.008 65.646 10.638
## 13 fit.models 7 3 65.646 NA NAprint(setdiff(names(glb_trnobs_df), names(glb_allobs_df)))## character(0)print(setdiff(names(glb_fitobs_df), names(glb_allobs_df)))## character(0)print(setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))## [1] "Privacy.Importance.predict.Low.cor.X.lm"
## [2] "Privacy.Importance.predict.Low.cor.X.lm.err"
## [3] "Privacy.Importance.predict.Low.cor.X.lm.accurate"for (col in setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))
# Merge or cbind ?
glb_allobs_df[glb_allobs_df$.lcn == "OOB", col] <- glb_OOBobs_df[, col]
print(setdiff(names(glb_newobs_df), names(glb_allobs_df)))## character(0)if (glb_save_envir)
save(glb_feats_df,
glb_allobs_df, #glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
glb_models_df, dsp_models_df, glb_models_lst, glb_sel_mdl, glb_sel_mdl_id,
glb_model_type,
file=paste0(glb_out_pfx, "selmdl_dsk.RData"))
#load(paste0(glb_out_pfx, "selmdl_dsk.RData"))
rm(ret_lst)## Warning in rm(ret_lst): object 'ret_lst' not foundreplay.petrisim(pn=glb_analytics_pn,
replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs,
"model.selected")), flip_coord=TRUE)## time trans "bgn " "fit.data.training.all " "predict.data.new " "end "
## 0.0000 multiple enabled transitions: data.training.all data.new model.selected firing: data.training.all
## 1.0000 1 2 1 0 0
## 1.0000 multiple enabled transitions: data.training.all data.new model.selected model.final data.training.all.prediction firing: data.new
## 2.0000 2 1 1 1 0
## 2.0000 multiple enabled transitions: data.training.all data.new model.selected model.final data.training.all.prediction data.new.prediction firing: model.selected
## 3.0000 3 0 2 1 0
glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.data.training", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 13 fit.models 7 3 65.646 70.767 5.121
## 14 fit.data.training 8 0 70.768 NA NAStep 8.0: fit data training
#load(paste0(glb_inp_pfx, "dsk.RData"))
# To create specific models
# glb_fin_mdl_id <- NULL; glb_fin_mdl <- NULL;
# glb_sel_mdl_id <- "Conditional.X.cp.0.rpart";
# glb_sel_mdl <- glb_models_lst[[glb_sel_mdl_id]]; print(glb_sel_mdl)
if (!is.null(glb_fin_mdl_id) && (glb_fin_mdl_id %in% names(glb_models_lst))) {
warning("Final model same as user selected model")
glb_fin_mdl <- glb_sel_mdl
} else {
# print(mdl_feats_df <- myextract_mdl_feats(sel_mdl=glb_sel_mdl,
# entity_df=glb_fitobs_df))
if ((model_method <- glb_sel_mdl$method) == "custom")
# get actual method from the model_id
model_method <- tail(unlist(strsplit(glb_sel_mdl_id, "[.]")), 1)
tune_finmdl_df <- NULL
if (nrow(glb_sel_mdl$bestTune) > 0) {
for (param in names(glb_sel_mdl$bestTune)) {
#print(sprintf("param: %s", param))
if (glb_sel_mdl$bestTune[1, param] != "none")
tune_finmdl_df <- rbind(tune_finmdl_df,
data.frame(parameter=param,
min=glb_sel_mdl$bestTune[1, param],
max=glb_sel_mdl$bestTune[1, param],
by=1)) # by val does not matter
}
}
# Sync with parameters in mydsutils.R
require(gdata)
ret_lst <- myfit_mdl(model_id="Final", model_method=model_method,
indep_vars_vctr=trim(unlist(strsplit(glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"feats"], "[,]"))),
model_type=glb_model_type,
rsp_var=glb_rsp_var, rsp_var_out=glb_rsp_var_out,
fit_df=glb_trnobs_df, OOB_df=NULL,
n_cv_folds=glb_n_cv_folds, tune_models_df=tune_finmdl_df,
# Automate from here
# Issues if glb_sel_mdl$method == "rf" b/c trainControl is "oob"; not "cv"
model_loss_mtrx=glb_model_metric_terms,
model_summaryFunction=glb_sel_mdl$control$summaryFunction,
model_metric=glb_sel_mdl$metric,
model_metric_maximize=glb_sel_mdl$maximize)
glb_fin_mdl <- glb_models_lst[[length(glb_models_lst)]]
glb_fin_mdl_id <- glb_models_df[length(glb_models_lst), "model_id"]
}## Loading required package: gdata
## gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
##
## gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
##
## Attaching package: 'gdata'
##
## The following object is masked from 'package:randomForest':
##
## combine
##
## The following objects are masked from 'package:dplyr':
##
## combine, first, last
##
## The following object is masked from 'package:stats':
##
## nobs
##
## The following object is masked from 'package:utils':
##
## object.size## [1] "fitting model: Final.lm"
## [1] " indep_vars: Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr"
## Aggregating results
## Fitting final model on full training set
## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced## Warning in sqrt(crit * p * (1 - hh)/hh): NaNs produced##
## Call:
## lm(formula = .outcome ~ ., data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -76.048 -19.249 4.149 21.387 65.612
##
## Coefficients: (1 not defined because of singularities)
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 34.9170 12.4594 2.802 0.00526
## Worry.About.Info.my.fctr1 13.7799 2.6606 5.179 3.20e-07
## Worry.About.Info.my.fctrNA.my -57.2029 30.1759 -1.896 0.05856
## `Age.my.fctr(33.6,49.2]` 11.0518 3.7471 2.949 0.00333
## `Age.my.fctr(49.2,64.8]` 10.9517 3.4654 3.160 0.00167
## `Age.my.fctr(64.8,80.4]` 1.8203 4.3536 0.418 0.67604
## `Age.my.fctr(80.4,96.1]` 2.4955 9.2478 0.270 0.78738
## Age.my.fctrNA.my 14.7688 8.7521 1.687 0.09212
## Tried.Masking.Identity.my.fctr1 4.6212 3.5949 1.285 0.19920
## Tried.Masking.Identity.my.fctrNA.my -6.8003 13.4700 -0.505 0.61388
## Internet.Use.my 17.9850 9.8992 1.817 0.06982
## Sex.fctrFemale 2.2626 2.6248 0.862 0.38909
## Conservativeness.my.fctr2 0.8528 6.4467 0.132 0.89481
## Conservativeness.my.fctr3 5.3331 5.9749 0.893 0.37249
## Conservativeness.my.fctr4 4.5422 5.9929 0.758 0.44884
## Conservativeness.my.fctr5 3.9890 7.0603 0.565 0.57232
## Conservativeness.my.fctrNA.my 5.1013 7.9028 0.646 0.51888
## Smartphone.my.fctr1 2.6720 2.9600 0.903 0.36709
## Smartphone.my.fctrNA.my 0.6564 8.4128 0.078 0.93784
## .rnorm -0.1930 1.2831 -0.150 0.88049
## Info.On.Internet.my.fctr1 -0.7005 5.4397 -0.129 0.89759
## Info.On.Internet.my.fctr10 -20.7025 10.8093 -1.915 0.05601
## Info.On.Internet.my.fctr11 16.5327 13.7849 1.199 0.23095
## Info.On.Internet.my.fctr2 -10.2710 5.0344 -2.040 0.04184
## Info.On.Internet.my.fctr3 -7.8068 5.1808 -1.507 0.13245
## Info.On.Internet.my.fctr4 -8.5032 5.0476 -1.685 0.09267
## Info.On.Internet.my.fctr5 -6.3418 5.4519 -1.163 0.24527
## Info.On.Internet.my.fctr6 -7.9571 5.8301 -1.365 0.17290
## Info.On.Internet.my.fctr7 -9.1325 5.8907 -1.550 0.12167
## Info.On.Internet.my.fctr8 4.3286 6.6599 0.650 0.51602
## Info.On.Internet.my.fctr9 -7.5259 9.1857 -0.819 0.41299
## Info.On.Internet.my.fctrNA.my NA NA NA NA
## Region.fctrSouth 2.2245 4.0273 0.552 0.58094
## Region.fctrWest 0.1380 4.2571 0.032 0.97414
## Region.fctrMidwest -0.2835 4.3720 -0.065 0.94832
## Anonymity.Possible.my.fctr1 -3.8693 2.6915 -1.438 0.15115
## Anonymity.Possible.my.fctrNA.my 1.9033 6.1261 0.311 0.75617
## Privacy.Laws.Effective.my.fctr1 -14.8815 3.1009 -4.799 2.09e-06
## Privacy.Laws.Effective.my.fctrNA.my -6.7398 4.7663 -1.414 0.15795
##
## (Intercept) **
## Worry.About.Info.my.fctr1 ***
## Worry.About.Info.my.fctrNA.my .
## `Age.my.fctr(33.6,49.2]` **
## `Age.my.fctr(49.2,64.8]` **
## `Age.my.fctr(64.8,80.4]`
## `Age.my.fctr(80.4,96.1]`
## Age.my.fctrNA.my .
## Tried.Masking.Identity.my.fctr1
## Tried.Masking.Identity.my.fctrNA.my
## Internet.Use.my .
## Sex.fctrFemale
## Conservativeness.my.fctr2
## Conservativeness.my.fctr3
## Conservativeness.my.fctr4
## Conservativeness.my.fctr5
## Conservativeness.my.fctrNA.my
## Smartphone.my.fctr1
## Smartphone.my.fctrNA.my
## .rnorm
## Info.On.Internet.my.fctr1
## Info.On.Internet.my.fctr10 .
## Info.On.Internet.my.fctr11
## Info.On.Internet.my.fctr2 *
## Info.On.Internet.my.fctr3
## Info.On.Internet.my.fctr4 .
## Info.On.Internet.my.fctr5
## Info.On.Internet.my.fctr6
## Info.On.Internet.my.fctr7
## Info.On.Internet.my.fctr8
## Info.On.Internet.my.fctr9
## Info.On.Internet.my.fctrNA.my
## Region.fctrSouth
## Region.fctrWest
## Region.fctrMidwest
## Anonymity.Possible.my.fctr1
## Anonymity.Possible.my.fctrNA.my
## Privacy.Laws.Effective.my.fctr1 ***
## Privacy.Laws.Effective.my.fctrNA.my
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 29.24 on 518 degrees of freedom
## Multiple R-squared: 0.1977, Adjusted R-squared: 0.1404
## F-statistic: 3.449 on 37 and 518 DF, p-value: 2.31e-10
##
## [1] " calling mypredict_mdl for fit:"## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading
## model_id model_method
## 1 Final.lm lm
## feats
## 1 Worry.About.Info.my.fctr, Age.my.fctr, Tried.Masking.Identity.my.fctr, Internet.Use.my, Sex.fctr, Conservativeness.my.fctr, Smartphone.my.fctr, .rnorm, Info.On.Internet.my.fctr, Region.fctr, Anonymity.Possible.my.fctr, Privacy.Laws.Effective.my.fctr
## max.nTuningRuns min.elapsedtime.everything min.elapsedtime.final
## 1 1 1.029 0.015
## max.R.sq.fit min.RMSE.fit max.Adj.R.sq.fit max.Rsquared.fit
## 1 0.1976727 31.31739 0.1403636 0.07528015
## min.RMSESD.fit max.RsquaredSD.fit
## 1 1.469406 0.02687989rm(ret_lst)
glb_chunks_df <- myadd_chunk(glb_chunks_df, "fit.data.training", major.inc=FALSE)## label step_major step_minor bgn end elapsed
## 14 fit.data.training 8 0 70.768 78.034 7.266
## 15 fit.data.training 8 1 78.035 NA NAglb_trnobs_df <- glb_get_predictions(df=glb_trnobs_df, mdl_id=glb_fin_mdl_id,
rsp_var_out=glb_rsp_var_out,
prob_threshold_def=ifelse(glb_is_classification && glb_is_binomial,
glb_models_df[glb_models_df$model_id == glb_sel_mdl_id, "opt.prob.threshold.OOB"], NULL))## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading
## Internet.Use Smartphone Sex Age State Region
## 487 1 0 Female NA Kentucky South
## 262 1 0 Male 66 Tennessee South
## 14 1 1 Female 47 North Carolina South
## 967 1 1 Male 50 California West
## 698 1 0 Male 60 Louisiana South
## 408 1 1 Female 60 Tennessee South
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 487 4 1 0 0.0
## 262 4 1 1 0.0
## 14 3 0 0 0.0
## 967 4 1 1 12.5
## 698 5 0 0 0.0
## 408 5 4 0 0.0
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 487 0 0 0
## 262 0 0 0
## 14 1 0 0
## 967 0 0 0
## 698 0 0 0
## 408 0 0 0
## .rownames .src .rnorm Internet.Use.my Age.my.fctr
## 487 487 Train -0.2531848 1 NA.my
## 262 262 Train -0.5622947 1 (64.8,80.4]
## 14 14 Train 0.7036249 1 (33.6,49.2]
## 967 967 Train 0.7633980 1 (49.2,64.8]
## 698 698 Train -1.0376304 1 (49.2,64.8]
## 408 408 Train -2.2727122 1 (49.2,64.8]
## Anonymity.Possible.my.fctr Conservativeness.my.fctr
## 487 0 4
## 262 0 4
## 14 1 3
## 967 0 4
## 698 0 5
## 408 0 5
## Info.On.Internet.my.fctr Privacy.Laws.Effective.my.fctr
## 487 1 0
## 262 1 0
## 14 0 0
## 967 1 0
## 698 0 0
## 408 4 0
## Smartphone.my.fctr Tried.Masking.Identity.my.fctr
## 487 0 0
## 262 0 0
## 14 1 0
## 967 1 0
## 698 0 0
## 408 1 0
## Worry.About.Info.my.fctr Sex.fctr State.fctr Region.fctr
## 487 0 Female Kentucky South
## 262 1 Male Tennessee South
## 14 0 Female North Carolina South
## 967 1 Male California West
## 698 0 Male Louisiana South
## 408 0 Female Tennessee South
## Privacy.Importance.predict.Final.lm
## 487 76.04835
## 262 74.67681
## 14 72.44079
## 967 84.13790
## 698 70.26737
## 408 66.93714
## Privacy.Importance.predict.Final.lm.err
## 487 76.04835
## 262 74.67681
## 14 72.44079
## 967 71.63790
## 698 70.26737
## 408 66.93714sav_featsimp_df <- glb_featsimp_df
#glb_feats_df <- sav_feats_df
# glb_feats_df <- mymerge_feats_importance(feats_df=glb_feats_df, sel_mdl=glb_fin_mdl,
# entity_df=glb_trnobs_df)
glb_featsimp_df <- myget_feats_importance(mdl=glb_fin_mdl, featsimp_df=glb_featsimp_df)
glb_featsimp_df[, paste0(glb_fin_mdl_id, ".importance")] <- glb_featsimp_df$importance
print(glb_featsimp_df)## Low.cor.X.lm.importance importance
## Worry.About.Info.my.fctr1 100.0000000 100.0000000
## Privacy.Laws.Effective.my.fctr1 92.6128304 92.6128304
## `Age.my.fctr(49.2,64.8]` 60.7732556 60.7732556
## `Age.my.fctr(33.6,49.2]` 56.6756161 56.6756161
## Info.On.Internet.my.fctr2 39.0097635 39.0097635
## Info.On.Internet.my.fctr10 36.5824483 36.5824483
## Worry.About.Info.my.fctrNA.my 36.2015544 36.2015544
## Internet.Use.my 34.6695694 34.6695694
## Age.my.fctrNA.my 32.1563634 32.1563634
## Info.On.Internet.my.fctr4 32.1007392 32.1007392
## Info.On.Internet.my.fctr7 29.4920157 29.4920157
## Info.On.Internet.my.fctr3 28.6475914 28.6475914
## Anonymity.Possible.my.fctr1 27.3021584 27.3021584
## Privacy.Laws.Effective.my.fctrNA.my 26.8441377 26.8441377
## Info.On.Internet.my.fctr6 25.8877833 25.8877833
## Tried.Masking.Identity.my.fctr1 24.3459375 24.3459375
## Info.On.Internet.my.fctr11 22.6724300 22.6724300
## Info.On.Internet.my.fctr5 21.9709901 21.9709901
## Smartphone.my.fctr1 16.9094201 16.9094201
## Conservativeness.my.fctr3 16.7124321 16.7124321
## Sex.fctrFemale 16.1181262 16.1181262
## Info.On.Internet.my.fctr9 15.2886330 15.2886330
## Conservativeness.my.fctr4 14.0961369 14.0961369
## Info.On.Internet.my.fctr8 11.9980054 11.9980054
## Conservativeness.my.fctrNA.my 11.9118764 11.9118764
## Conservativeness.my.fctr5 10.3474601 10.3474601
## Region.fctrSouth 10.1019949 10.1019949
## Tried.Masking.Identity.my.fctrNA.my 9.1788768 9.1788768
## `Age.my.fctr(64.8,80.4]` 7.4936724 7.4936724
## Anonymity.Possible.my.fctrNA.my 5.4063607 5.4063607
## `Age.my.fctr(80.4,96.1]` 4.6130643 4.6130643
## .rnorm 2.2924783 2.2924783
## Conservativeness.my.fctr2 1.9402339 1.9402339
## Info.On.Internet.my.fctr1 1.8719519 1.8719519
## Smartphone.my.fctrNA.my 0.8859963 0.8859963
## Region.fctrMidwest 0.6299939 0.6299939
## Region.fctrWest 0.0000000 0.0000000
## Final.lm.importance
## Worry.About.Info.my.fctr1 100.0000000
## Privacy.Laws.Effective.my.fctr1 92.6128304
## `Age.my.fctr(49.2,64.8]` 60.7732556
## `Age.my.fctr(33.6,49.2]` 56.6756161
## Info.On.Internet.my.fctr2 39.0097635
## Info.On.Internet.my.fctr10 36.5824483
## Worry.About.Info.my.fctrNA.my 36.2015544
## Internet.Use.my 34.6695694
## Age.my.fctrNA.my 32.1563634
## Info.On.Internet.my.fctr4 32.1007392
## Info.On.Internet.my.fctr7 29.4920157
## Info.On.Internet.my.fctr3 28.6475914
## Anonymity.Possible.my.fctr1 27.3021584
## Privacy.Laws.Effective.my.fctrNA.my 26.8441377
## Info.On.Internet.my.fctr6 25.8877833
## Tried.Masking.Identity.my.fctr1 24.3459375
## Info.On.Internet.my.fctr11 22.6724300
## Info.On.Internet.my.fctr5 21.9709901
## Smartphone.my.fctr1 16.9094201
## Conservativeness.my.fctr3 16.7124321
## Sex.fctrFemale 16.1181262
## Info.On.Internet.my.fctr9 15.2886330
## Conservativeness.my.fctr4 14.0961369
## Info.On.Internet.my.fctr8 11.9980054
## Conservativeness.my.fctrNA.my 11.9118764
## Conservativeness.my.fctr5 10.3474601
## Region.fctrSouth 10.1019949
## Tried.Masking.Identity.my.fctrNA.my 9.1788768
## `Age.my.fctr(64.8,80.4]` 7.4936724
## Anonymity.Possible.my.fctrNA.my 5.4063607
## `Age.my.fctr(80.4,96.1]` 4.6130643
## .rnorm 2.2924783
## Conservativeness.my.fctr2 1.9402339
## Info.On.Internet.my.fctr1 1.8719519
## Smartphone.my.fctrNA.my 0.8859963
## Region.fctrMidwest 0.6299939
## Region.fctrWest 0.0000000if (glb_is_classification && glb_is_binomial)
glb_analytics_diag_plots(obs_df=glb_trnobs_df, mdl_id=glb_fin_mdl_id,
prob_threshold=glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"opt.prob.threshold.OOB"]) else
glb_analytics_diag_plots(obs_df=glb_trnobs_df, mdl_id=glb_fin_mdl_id) ## Warning in glb_analytics_diag_plots(obs_df = glb_trnobs_df, mdl_id =
## glb_fin_mdl_id): Limiting important feature scatter plots to 5 out of 12
## Internet.Use Smartphone Sex Age State Region
## 487 1 0 Female NA Kentucky South
## 262 1 0 Male 66 Tennessee South
## 14 1 1 Female 47 North Carolina South
## 967 1 1 Male 50 California West
## 698 1 0 Male 60 Louisiana South
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 487 4 1 0 0.0
## 262 4 1 1 0.0
## 14 3 0 0 0.0
## 967 4 1 1 12.5
## 698 5 0 0 0.0
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 487 0 0 0
## 262 0 0 0
## 14 1 0 0
## 967 0 0 0
## 698 0 0 0
## .rownames .src .rnorm Internet.Use.my Age.my.fctr
## 487 487 Train -0.2531848 1 NA.my
## 262 262 Train -0.5622947 1 (64.8,80.4]
## 14 14 Train 0.7036249 1 (33.6,49.2]
## 967 967 Train 0.7633980 1 (49.2,64.8]
## 698 698 Train -1.0376304 1 (49.2,64.8]
## Anonymity.Possible.my.fctr Conservativeness.my.fctr
## 487 0 4
## 262 0 4
## 14 1 3
## 967 0 4
## 698 0 5
## Info.On.Internet.my.fctr Privacy.Laws.Effective.my.fctr
## 487 1 0
## 262 1 0
## 14 0 0
## 967 1 0
## 698 0 0
## Smartphone.my.fctr Tried.Masking.Identity.my.fctr
## 487 0 0
## 262 0 0
## 14 1 0
## 967 1 0
## 698 0 0
## Worry.About.Info.my.fctr Sex.fctr State.fctr Region.fctr
## 487 0 Female Kentucky South
## 262 1 Male Tennessee South
## 14 0 Female North Carolina South
## 967 1 Male California West
## 698 0 Male Louisiana South
## Privacy.Importance.predict.Final.lm
## 487 76.04835
## 262 74.67681
## 14 72.44079
## 967 84.13790
## 698 70.26737
## Privacy.Importance.predict.Final.lm.err .label
## 487 76.04835 487
## 262 74.67681 262
## 14 72.44079 14
## 967 71.63790 967
## 698 70.26737 698
dsp_feats_vctr <- c(NULL)
for(var in grep(".importance", names(glb_feats_df), fixed=TRUE, value=TRUE))
dsp_feats_vctr <- union(dsp_feats_vctr,
glb_feats_df[!is.na(glb_feats_df[, var]), "id"])
print(glb_trnobs_df[glb_trnobs_df$UniqueID %in% FN_OOB_ids,
grep(glb_rsp_var, names(glb_trnobs_df), value=TRUE)])## [1] Privacy.Importance
## [2] Privacy.Importance.predict.Final.lm
## [3] Privacy.Importance.predict.Final.lm.err
## <0 rows> (or 0-length row.names)print(setdiff(names(glb_trnobs_df), names(glb_allobs_df)))## [1] "Privacy.Importance.predict.Final.lm"
## [2] "Privacy.Importance.predict.Final.lm.err"for (col in setdiff(names(glb_trnobs_df), names(glb_allobs_df)))
# Merge or cbind ?
glb_allobs_df[glb_allobs_df$.src == "Train", col] <- glb_trnobs_df[, col]
print(setdiff(names(glb_fitobs_df), names(glb_allobs_df)))## character(0)print(setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))## character(0)for (col in setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))
# Merge or cbind ?
glb_allobs_df[glb_allobs_df$.lcn == "OOB", col] <- glb_OOBobs_df[, col]
print(setdiff(names(glb_newobs_df), names(glb_allobs_df)))## character(0)if (glb_save_envir)
save(glb_feats_df, glb_allobs_df,
#glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
glb_models_df, dsp_models_df, glb_models_lst, glb_model_type,
glb_sel_mdl, glb_sel_mdl_id,
glb_fin_mdl, glb_fin_mdl_id,
file=paste0(glb_out_pfx, "dsk.RData"))
replay.petrisim(pn=glb_analytics_pn,
replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs,
"data.training.all.prediction","model.final")), flip_coord=TRUE)## time trans "bgn " "fit.data.training.all " "predict.data.new " "end "
## 0.0000 multiple enabled transitions: data.training.all data.new model.selected firing: data.training.all
## 1.0000 1 2 1 0 0
## 1.0000 multiple enabled transitions: data.training.all data.new model.selected model.final data.training.all.prediction firing: data.new
## 2.0000 2 1 1 1 0
## 2.0000 multiple enabled transitions: data.training.all data.new model.selected model.final data.training.all.prediction data.new.prediction firing: model.selected
## 3.0000 3 0 2 1 0
## 3.0000 multiple enabled transitions: model.final data.training.all.prediction data.new.prediction firing: data.training.all.prediction
## 4.0000 5 0 1 1 1
## 4.0000 multiple enabled transitions: model.final data.training.all.prediction data.new.prediction firing: model.final
## 5.0000 4 0 0 2 1
glb_chunks_df <- myadd_chunk(glb_chunks_df, "predict.data.new", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 15 fit.data.training 8 1 78.035 82.865 4.83
## 16 predict.data.new 9 0 82.865 NA NAStep 9.0: predict data new
# Compute final model predictions
glb_newobs_df <- glb_get_predictions(glb_newobs_df, mdl_id=glb_fin_mdl_id,
rsp_var_out=glb_rsp_var_out,
prob_threshold_def=ifelse(glb_is_classification && glb_is_binomial,
glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"opt.prob.threshold.OOB"], NULL))## Warning in predict.lm(modelFit, newdata): prediction from a rank-deficient
## fit may be misleading## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (stat_smooth).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Internet.Use Smartphone Sex Age State Region
## 794 1 1 Female 49 Virginia South
## 80 1 0 Male 21 Florida South
## 683 1 1 Male 43 North Carolina South
## 460 1 0 Female 62 Virginia South
## 954 1 1 Female 62 Florida South
## 632 1 0 Female 55 Alabama South
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 794 3 0 1 11.11111
## 80 3 8 1 0.00000
## 683 3 0 0 0.00000
## 460 2 8 1 0.00000
## 954 4 3 0 0.00000
## 632 2 0 0 0.00000
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 794 1 0 0
## 80 1 0 0
## 683 0 0 0
## 460 0 0 1
## 954 NA 0 0
## 632 0 0 0
## .rownames .src .rnorm Internet.Use.my Age.my.fctr
## 794 794 Test -0.3440475 1 (33.6,49.2]
## 80 80 Test 0.5643370 1 (17.9,33.6]
## 683 683 Test -0.3761202 1 (33.6,49.2]
## 460 460 Test -1.1358528 1 (49.2,64.8]
## 954 954 Test 0.3327613 1 (49.2,64.8]
## 632 632 Test -0.6707990 1 (49.2,64.8]
## Anonymity.Possible.my.fctr Conservativeness.my.fctr
## 794 1 3
## 80 1 3
## 683 0 3
## 460 0 2
## 954 NA.my 4
## 632 0 2
## Info.On.Internet.my.fctr Privacy.Laws.Effective.my.fctr
## 794 0 0
## 80 8 0
## 683 0 0
## 460 8 1
## 954 3 0
## 632 0 0
## Smartphone.my.fctr Tried.Masking.Identity.my.fctr
## 794 1 0
## 80 0 0
## 683 1 0
## 460 0 0
## 954 1 0
## 632 0 0
## Worry.About.Info.my.fctr Sex.fctr State.fctr Region.fctr
## 794 1 Female Virginia South
## 80 1 Male Florida South
## 683 0 Male North Carolina South
## 460 1 Female Virginia South
## 954 0 Female Florida South
## 632 0 Female Alabama South
## Privacy.Importance.predict.Final.lm
## 794 86.42286
## 80 74.58973
## 683 74.25595
## 460 72.63961
## 954 69.58716
## 632 69.32296
## Privacy.Importance.predict.Final.lm.err
## 794 75.31175
## 80 74.58973
## 683 74.25595
## 460 72.63961
## 954 69.58716
## 632 69.32296if (glb_is_classification && glb_is_binomial)
glb_analytics_diag_plots(obs_df=glb_newobs_df, mdl_id=glb_fin_mdl_id,
prob_threshold=glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"opt.prob.threshold.OOB"]) else
glb_analytics_diag_plots(obs_df=glb_newobs_df, mdl_id=glb_fin_mdl_id) ## Warning in glb_analytics_diag_plots(obs_df = glb_newobs_df, mdl_id =
## glb_fin_mdl_id): Limiting important feature scatter plots to 5 out of 12## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
## Internet.Use Smartphone Sex Age State Region
## 794 1 1 Female 49 Virginia South
## 80 1 0 Male 21 Florida South
## 683 1 1 Male 43 North Carolina South
## 460 1 0 Female 62 Virginia South
## 954 1 1 Female 62 Florida South
## Conservativeness Info.On.Internet Worry.About.Info Privacy.Importance
## 794 3 0 1 11.11111
## 80 3 8 1 0.00000
## 683 3 0 0 0.00000
## 460 2 8 1 0.00000
## 954 4 3 0 0.00000
## Anonymity.Possible Tried.Masking.Identity Privacy.Laws.Effective
## 794 1 0 0
## 80 1 0 0
## 683 0 0 0
## 460 0 0 1
## 954 NA 0 0
## .rownames .src .rnorm Internet.Use.my Age.my.fctr
## 794 794 Test -0.3440475 1 (33.6,49.2]
## 80 80 Test 0.5643370 1 (17.9,33.6]
## 683 683 Test -0.3761202 1 (33.6,49.2]
## 460 460 Test -1.1358528 1 (49.2,64.8]
## 954 954 Test 0.3327613 1 (49.2,64.8]
## Anonymity.Possible.my.fctr Conservativeness.my.fctr
## 794 1 3
## 80 1 3
## 683 0 3
## 460 0 2
## 954 NA.my 4
## Info.On.Internet.my.fctr Privacy.Laws.Effective.my.fctr
## 794 0 0
## 80 8 0
## 683 0 0
## 460 8 1
## 954 3 0
## Smartphone.my.fctr Tried.Masking.Identity.my.fctr
## 794 1 0
## 80 0 0
## 683 1 0
## 460 0 0
## 954 1 0
## Worry.About.Info.my.fctr Sex.fctr State.fctr Region.fctr
## 794 1 Female Virginia South
## 80 1 Male Florida South
## 683 0 Male North Carolina South
## 460 1 Female Virginia South
## 954 0 Female Florida South
## Privacy.Importance.predict.Final.lm
## 794 86.42286
## 80 74.58973
## 683 74.25595
## 460 72.63961
## 954 69.58716
## Privacy.Importance.predict.Final.lm.err .label
## 794 75.31175 794
## 80 74.58973 80
## 683 74.25595 683
## 460 72.63961 460
## 954 69.58716 954## Warning in loop_apply(n, do.ply): Removed 215 rows containing missing
## values (geom_point).
if (glb_is_classification && glb_is_binomial) {
submit_df <- glb_newobs_df[, c(glb_id_var,
paste0(glb_rsp_var_out, glb_fin_mdl_id, ".prob"))]
names(submit_df)[2] <- "Probability1"
} else submit_df <- glb_newobs_df[, c(glb_id_var,
paste0(glb_rsp_var_out, glb_fin_mdl_id))]
write.csv(submit_df,
paste0(gsub(".", "_", paste0(glb_out_pfx, glb_fin_mdl_id), fixed=TRUE),
"_submit.csv"), row.names=FALSE)
# print(orderBy(~ -max.auc.OOB, glb_models_df[, c("model_id",
# "max.auc.OOB", "max.Accuracy.OOB")]))
if (glb_is_classification && glb_is_binomial)
print(glb_models_df[glb_models_df$model_id == glb_sel_mdl_id,
"opt.prob.threshold.OOB"])
print(sprintf("glb_sel_mdl_id: %s", glb_sel_mdl_id))## [1] "glb_sel_mdl_id: Low.cor.X.lm"print(sprintf("glb_fin_mdl_id: %s", glb_fin_mdl_id))## [1] "glb_fin_mdl_id: Final.lm"print(dim(glb_fitobs_df))## [1] 556 28print(dsp_models_df)## model_id min.RMSE.OOB max.R.sq.OOB max.Adj.R.sq.fit
## 6 Low.cor.X.lm NA NA 0.140363573
## 7 All.X.lm NA NA 0.140363573
## 5 Max.cor.Y.lm NA NA 0.117228253
## 1 MFO.lm NA NA -0.001791565
## 2 Max.cor.Y.cv.0.rpart NA NA NA
## 3 Max.cor.Y.cv.0.cp.0.rpart NA NA NA
## 4 Max.cor.Y.rpart NA NA NA
## 8 All.X.glm NA NA NA
## 9 All.X.bayesglm NA NA NA
## 10 All.X.no.rnorm.rpart NA NA NA
## 11 All.X.no.rnorm.rf NA NA NAif (glb_is_classification) {
print(sprintf("%s OOB confusion matrix & accuracy: ", glb_sel_mdl_id))
print(t(confusionMatrix(glb_OOBobs_df[, paste0(glb_rsp_var_out, glb_sel_mdl_id)],
glb_OOBobs_df[, glb_rsp_var])$table))
if (!is.null(glb_category_vars)) {
tmp_OOBobs_df <- glb_OOBobs_df[, c(glb_category_vars, predct_accurate_var_name)]
names(tmp_OOBobs_df)[length(names(tmp_OOBobs_df))] <- "accurate.OOB"
aOOB_ctgry_df <- mycreate_xtab_df(tmp_OOBobs_df, names(tmp_OOBobs_df))
aOOB_ctgry_df[is.na(aOOB_ctgry_df)] <- 0
aOOB_ctgry_df <- mutate(aOOB_ctgry_df,
.n.OOB = accurate.OOB.FALSE + accurate.OOB.TRUE,
max.accuracy.OOB = accurate.OOB.TRUE / .n.OOB)
#intersect(names(glb_ctgry_df), names(aOOB_ctgry_df))
glb_ctgry_df <- merge(glb_ctgry_df, aOOB_ctgry_df, all=TRUE)
print(orderBy(~-accurate.OOB.FALSE, glb_ctgry_df))
}
}
dsp_myCategory_conf_mtrx <- function(myCategory) {
print(sprintf("%s OOB::myCategory=%s confusion matrix & accuracy: ",
glb_sel_mdl_id, myCategory))
print(t(confusionMatrix(
glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory,
paste0(glb_rsp_var_out, glb_sel_mdl_id)],
glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory, glb_rsp_var])$table))
print(sum(glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory,
predct_accurate_var_name]) /
nrow(glb_OOBobs_df[glb_OOBobs_df$myCategory == myCategory, ]))
err_ids <- glb_OOBobs_df[(glb_OOBobs_df$myCategory == myCategory) &
(!glb_OOBobs_df[, predct_accurate_var_name]), glb_id_var]
OOB_FNerr_df <- glb_OOBobs_df[(glb_OOBobs_df$UniqueID %in% err_ids) &
(glb_OOBobs_df$Popular == 1),
c(
".clusterid",
"Popular", "Headline", "Snippet", "Abstract")]
print(sprintf("%s OOB::myCategory=%s FN errors: %d", glb_sel_mdl_id, myCategory,
nrow(OOB_FNerr_df)))
print(OOB_FNerr_df)
OOB_FPerr_df <- glb_OOBobs_df[(glb_OOBobs_df$UniqueID %in% err_ids) &
(glb_OOBobs_df$Popular == 0),
c(
".clusterid",
"Popular", "Headline", "Snippet", "Abstract")]
print(sprintf("%s OOB::myCategory=%s FP errors: %d", glb_sel_mdl_id, myCategory,
nrow(OOB_FPerr_df)))
print(OOB_FPerr_df)
}
#dsp_myCategory_conf_mtrx(myCategory="OpEd#Opinion#")
#dsp_myCategory_conf_mtrx(myCategory="Business#Business Day#Dealbook")
#dsp_myCategory_conf_mtrx(myCategory="##")
if (glb_is_classification) {
print("FN_OOB_ids:")
print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])
print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
glb_txt_vars])
print(dsp_vctr <- colSums(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
setdiff(grep("[HSA].", names(glb_OOBobs_df), value=TRUE),
union(myfind_chr_cols_df(glb_OOBobs_df),
grep(".fctr", names(glb_OOBobs_df), fixed=TRUE, value=TRUE)))]))
}
dsp_hdlpfx_results <- function(hdlpfx) {
print(hdlpfx)
print(glb_OOBobs_df[glb_OOBobs_df$Headline.pfx %in% c(hdlpfx),
grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])
print(glb_newobs_df[glb_newobs_df$Headline.pfx %in% c(hdlpfx),
grep(glb_rsp_var, names(glb_newobs_df), value=TRUE)])
print(dsp_vctr <- colSums(glb_newobs_df[glb_newobs_df$Headline.pfx %in% c(hdlpfx),
setdiff(grep("[HSA]\\.", names(glb_newobs_df), value=TRUE),
union(myfind_chr_cols_df(glb_newobs_df),
grep(".fctr", names(glb_newobs_df), fixed=TRUE, value=TRUE)))]))
print(dsp_vctr <- dsp_vctr[dsp_vctr != 0])
print(glb_newobs_df[glb_newobs_df$Headline.pfx %in% c(hdlpfx),
union(names(dsp_vctr), myfind_chr_cols_df(glb_newobs_df))])
}
#dsp_hdlpfx_results(hdlpfx="Ask Well::")
# print("myMisc::|OpEd|blank|blank|1:")
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% c(6446),
# grep(glb_rsp_var, names(glb_OOBobs_df), value=TRUE)])
# print(glb_OOBobs_df[glb_OOBobs_df$UniqueID %in% FN_OOB_ids,
# c("WordCount", "WordCount.log", "myMultimedia",
# "NewsDesk", "SectionName", "SubsectionName")])
# print(mycreate_sqlxtab_df(glb_allobs_df[sel_obs(Headline.contains="[Vv]ideo"), ],
# c(glb_rsp_var, "myMultimedia")))
# dsp_chisq.test(Headline.contains="[Vi]deo")
# print(glb_allobs_df[sel_obs(Headline.contains="[Vv]ideo"),
# c(glb_rsp_var, "Popular", "myMultimedia", "Headline")])
# print(glb_allobs_df[sel_obs(Headline.contains="[Ee]bola", Popular=1),
# c(glb_rsp_var, "Popular", "myMultimedia", "Headline",
# "NewsDesk", "SectionName", "SubsectionName")])
# print(subset(glb_feats_df, !is.na(importance))[,
# c("is.ConditionalX.y",
# grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
# print(subset(glb_feats_df, is.ConditionalX.y & is.na(importance))[,
# c("is.ConditionalX.y",
# grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
# print(subset(glb_feats_df, !is.na(importance))[,
# c("zeroVar", "nzv", "myNearZV",
# grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
# print(subset(glb_feats_df, is.na(importance))[,
# c("zeroVar", "nzv", "myNearZV",
# grep("importance", names(glb_feats_df), fixed=TRUE, value=TRUE))])
print(orderBy(as.formula(paste0("~ -", glb_sel_mdl_id, ".importance")), glb_featsimp_df))## Low.cor.X.lm.importance importance
## Worry.About.Info.my.fctr1 100.0000000 100.0000000
## Privacy.Laws.Effective.my.fctr1 92.6128304 92.6128304
## `Age.my.fctr(49.2,64.8]` 60.7732556 60.7732556
## `Age.my.fctr(33.6,49.2]` 56.6756161 56.6756161
## Info.On.Internet.my.fctr2 39.0097635 39.0097635
## Info.On.Internet.my.fctr10 36.5824483 36.5824483
## Worry.About.Info.my.fctrNA.my 36.2015544 36.2015544
## Internet.Use.my 34.6695694 34.6695694
## Age.my.fctrNA.my 32.1563634 32.1563634
## Info.On.Internet.my.fctr4 32.1007392 32.1007392
## Info.On.Internet.my.fctr7 29.4920157 29.4920157
## Info.On.Internet.my.fctr3 28.6475914 28.6475914
## Anonymity.Possible.my.fctr1 27.3021584 27.3021584
## Privacy.Laws.Effective.my.fctrNA.my 26.8441377 26.8441377
## Info.On.Internet.my.fctr6 25.8877833 25.8877833
## Tried.Masking.Identity.my.fctr1 24.3459375 24.3459375
## Info.On.Internet.my.fctr11 22.6724300 22.6724300
## Info.On.Internet.my.fctr5 21.9709901 21.9709901
## Smartphone.my.fctr1 16.9094201 16.9094201
## Conservativeness.my.fctr3 16.7124321 16.7124321
## Sex.fctrFemale 16.1181262 16.1181262
## Info.On.Internet.my.fctr9 15.2886330 15.2886330
## Conservativeness.my.fctr4 14.0961369 14.0961369
## Info.On.Internet.my.fctr8 11.9980054 11.9980054
## Conservativeness.my.fctrNA.my 11.9118764 11.9118764
## Conservativeness.my.fctr5 10.3474601 10.3474601
## Region.fctrSouth 10.1019949 10.1019949
## Tried.Masking.Identity.my.fctrNA.my 9.1788768 9.1788768
## `Age.my.fctr(64.8,80.4]` 7.4936724 7.4936724
## Anonymity.Possible.my.fctrNA.my 5.4063607 5.4063607
## `Age.my.fctr(80.4,96.1]` 4.6130643 4.6130643
## .rnorm 2.2924783 2.2924783
## Conservativeness.my.fctr2 1.9402339 1.9402339
## Info.On.Internet.my.fctr1 1.8719519 1.8719519
## Smartphone.my.fctrNA.my 0.8859963 0.8859963
## Region.fctrMidwest 0.6299939 0.6299939
## Region.fctrWest 0.0000000 0.0000000
## Final.lm.importance
## Worry.About.Info.my.fctr1 100.0000000
## Privacy.Laws.Effective.my.fctr1 92.6128304
## `Age.my.fctr(49.2,64.8]` 60.7732556
## `Age.my.fctr(33.6,49.2]` 56.6756161
## Info.On.Internet.my.fctr2 39.0097635
## Info.On.Internet.my.fctr10 36.5824483
## Worry.About.Info.my.fctrNA.my 36.2015544
## Internet.Use.my 34.6695694
## Age.my.fctrNA.my 32.1563634
## Info.On.Internet.my.fctr4 32.1007392
## Info.On.Internet.my.fctr7 29.4920157
## Info.On.Internet.my.fctr3 28.6475914
## Anonymity.Possible.my.fctr1 27.3021584
## Privacy.Laws.Effective.my.fctrNA.my 26.8441377
## Info.On.Internet.my.fctr6 25.8877833
## Tried.Masking.Identity.my.fctr1 24.3459375
## Info.On.Internet.my.fctr11 22.6724300
## Info.On.Internet.my.fctr5 21.9709901
## Smartphone.my.fctr1 16.9094201
## Conservativeness.my.fctr3 16.7124321
## Sex.fctrFemale 16.1181262
## Info.On.Internet.my.fctr9 15.2886330
## Conservativeness.my.fctr4 14.0961369
## Info.On.Internet.my.fctr8 11.9980054
## Conservativeness.my.fctrNA.my 11.9118764
## Conservativeness.my.fctr5 10.3474601
## Region.fctrSouth 10.1019949
## Tried.Masking.Identity.my.fctrNA.my 9.1788768
## `Age.my.fctr(64.8,80.4]` 7.4936724
## Anonymity.Possible.my.fctrNA.my 5.4063607
## `Age.my.fctr(80.4,96.1]` 4.6130643
## .rnorm 2.2924783
## Conservativeness.my.fctr2 1.9402339
## Info.On.Internet.my.fctr1 1.8719519
## Smartphone.my.fctrNA.my 0.8859963
## Region.fctrMidwest 0.6299939
## Region.fctrWest 0.0000000print(setdiff(names(glb_trnobs_df), names(glb_allobs_df)))## character(0)for (col in setdiff(names(glb_trnobs_df), names(glb_allobs_df)))
# Merge or cbind ?
glb_allobs_df[glb_allobs_df$.src == "Train", col] <- glb_trnobs_df[, col]
print(setdiff(names(glb_fitobs_df), names(glb_allobs_df)))## character(0)print(setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))## character(0)for (col in setdiff(names(glb_OOBobs_df), names(glb_allobs_df)))
# Merge or cbind ?
glb_allobs_df[glb_allobs_df$.lcn == "OOB", col] <- glb_OOBobs_df[, col]
print(setdiff(names(glb_newobs_df), names(glb_allobs_df)))## character(0)if (glb_save_envir)
save(glb_feats_df, glb_allobs_df,
#glb_trnobs_df, glb_fitobs_df, glb_OOBobs_df, glb_newobs_df,
glb_models_df, dsp_models_df, glb_models_lst, glb_model_type,
glb_sel_mdl, glb_sel_mdl_id,
glb_fin_mdl, glb_fin_mdl_id,
file=paste0(glb_out_pfx, "prdnew_dsk.RData"))
rm(submit_df, tmp_OOBobs_df)## Warning in rm(submit_df, tmp_OOBobs_df): object 'tmp_OOBobs_df' not found# tmp_replay_lst <- replay.petrisim(pn=glb_analytics_pn,
# replay.trans=(glb_analytics_avl_objs <- c(glb_analytics_avl_objs,
# "data.new.prediction")), flip_coord=TRUE)
# print(ggplot.petrinet(tmp_replay_lst[["pn"]]) + coord_flip())
glb_chunks_df <- myadd_chunk(glb_chunks_df, "display.session.info", major.inc=TRUE)## label step_major step_minor bgn end elapsed
## 16 predict.data.new 9 0 82.865 88.41 5.545
## 17 display.session.info 10 0 88.410 NA NANull Hypothesis (\(\sf{H_{0}}\)): mpg is not impacted by am_fctr.
The variance by am_fctr appears to be independent. #{r q1, cache=FALSE} # print(t.test(subset(cars_df, am_fctr == "automatic")$mpg, # subset(cars_df, am_fctr == "manual")$mpg, # var.equal=FALSE)$conf) # We reject the null hypothesis i.e. we have evidence to conclude that am_fctr impacts mpg (95% confidence). Manual transmission is better for miles per gallon versus automatic transmission.
## label step_major step_minor bgn end elapsed
## 11 fit.models 7 1 32.710 55.008 22.298
## 10 fit.models 7 0 20.175 32.709 12.535
## 12 fit.models 7 2 55.008 65.646 10.638
## 14 fit.data.training 8 0 70.768 78.034 7.266
## 2 inspect.data 2 0 9.966 15.619 5.653
## 16 predict.data.new 9 0 82.865 88.410 5.545
## 13 fit.models 7 3 65.646 70.767 5.121
## 15 fit.data.training 8 1 78.035 82.865 4.830
## 3 scrub.data 2 1 15.620 17.419 1.799
## 6 extract.features 3 0 17.639 18.980 1.342
## 1 import.data 1 0 9.118 9.966 0.848
## 8 select.features 5 0 19.253 19.878 0.626
## 9 partition.data.training 6 0 19.879 20.175 0.296
## 7 cluster.data 4 0 18.981 19.252 0.271
## 4 transform.data 2 2 17.420 17.556 0.136
## 5 manage.missing.data 2 3 17.556 17.639 0.083
## duration
## 11 22.298
## 10 12.534
## 12 10.638
## 14 7.266
## 2 5.653
## 16 5.545
## 13 5.121
## 15 4.830
## 3 1.799
## 6 1.341
## 1 0.848
## 8 0.625
## 9 0.296
## 7 0.271
## 4 0.136
## 5 0.083
## [1] "Total Elapsed Time: 88.41 secs"
## label step_major step_minor bgn end elapsed
## 6 fit.models_1_rf 6 0 45.066 55.002 9.936
## 5 fit.models_1_rpart 5 0 42.139 45.066 2.927
## 4 fit.models_1_bayesglm 4 0 39.446 42.138 2.692
## 3 fit.models_1_glm 3 0 36.768 39.446 2.678
## 2 fit.models_1_lm 2 0 34.345 36.768 2.423
## 1 fit.models_1_bgn 1 0 34.331 34.345 0.014
## duration
## 6 9.936
## 5 2.927
## 4 2.692
## 3 2.678
## 2 2.423
## 1 0.014
## [1] "Total Elapsed Time: 55.002 secs"
## R version 3.2.0 (2015-04-16)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.10.3 (Yosemite)
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] gdata_2.16.1 randomForest_4.6-10 arm_1.8-5
## [4] lme4_1.1-7 Rcpp_0.11.6 Matrix_1.2-1
## [7] MASS_7.3-40 rpart.plot_1.5.2 rpart_4.1-9
## [10] reshape2_1.4.1 mgcv_1.8-6 nlme_3.1-120
## [13] dplyr_0.4.1 plyr_1.8.2 caTools_1.17.1
## [16] doMC_1.3.3 iterators_1.0.7 foreach_1.4.2
## [19] doBy_4.5-13 survival_2.38-1 caret_6.0-47
## [22] ggplot2_1.0.1 lattice_0.20-31
##
## loaded via a namespace (and not attached):
## [1] gtools_3.5.0 splines_3.2.0 colorspace_1.2-6
## [4] htmltools_0.2.6 yaml_2.1.13 nloptr_1.0.4
## [7] DBI_0.3.1 RColorBrewer_1.1-2 stringr_1.0.0
## [10] munsell_0.4.2 gtable_0.1.2 codetools_0.2-11
## [13] coda_0.17-1 evaluate_0.7 labeling_0.3
## [16] knitr_1.10.5 SparseM_1.6 quantreg_5.11
## [19] pbkrtest_0.4-2 proto_0.3-10 scales_0.2.4
## [22] formatR_1.2 BradleyTerry2_1.0-6 abind_1.4-3
## [25] digest_0.6.8 stringi_0.4-1 brglm_0.5-9
## [28] tools_3.2.0 bitops_1.0-6 magrittr_1.5
## [31] lazyeval_0.1.10 car_2.0-25 assertthat_0.1
## [34] minqa_1.2.4 rmarkdown_0.6.1 nnet_7.3-9
## [37] compiler_3.2.0